Methods and Materials Relating to Breast Cancer Diagnosis

ABSTRACT

Classification of breast tumours into Estrogen Receptor positive and negative (ER+ and ER−) subtypes is an important distinction in the treatment of breast cancer. ER typing is frequently performed using expression profiles of genes whose expression is known to be affected by ER activity. Some tumours cannot confidently be assigned to a particular ER type based on such expression data. The present inventors have found that such “low confidence” tumours constitute a distinct biological subtype of breast tumours associated with significantly worse overall survival than high confidence tumours. Gene sets capable of distinguishing low confidence from high confidence tumours are provided, along with methods and apparatus for performing appropriate classification of breast tumours.

FIELD OF THE INVENTION

The present invention concerns materials and methods relating to the diagnosis of breast cancer. Particularly, the present invention concerns the diagnosis and/or classification of “low confidence” tumours which exhibit a significantly worse overall survival and shorter time to distant metastasis compared to their “high confidence” counterparts.

BACKGROUND OF THE INVENTION

There has been an intense interest in the use of gene expression data for biological classification, particularly in the fields of oncology and medicine. One exciting aspect of this approach has been its ability to define clinically relevant subtypes of cancer that have previously eluded more traditional light-microscopy approaches (15, 16). Despite this potential, a number of issues have to be resolved before the use of gene expression data for clinical diagnosis can become a reality. For example, algorithms need to be implemented that, besides delivering the correct classification, can also accurately determine the confidence of the prediction. This is particularly important if the classification affects the subsequent course of treatment—if furnished with such information, the treating physician can then weigh the confidence of prediction with the potential morbidity of a specific intervention to make an informed clinical choice.

The classification of breast tumours into Estrogen Receptor positive (ER+) and negative (ER−) subtypes is a critical distinction in the treatment of breast cancer. ER− tumours are in general more clinically aggressive than their ER+ counterparts, and ER+ tumours are routinely treated using anti-hormonal therapies such as tamoxifen (1). Presently, a tumour's ER status is routinely determined by immunohistochemistry (IHC) or immunoblotting using an antibody to ER. This technique, however, is imperfect—for example, it may fail to detect tumours harboring genetic alterations in ER that render it inactive or constitutively active (2). Thus, it is crucially important to develop more accurate methodologies to improve the ER subtype classification of breast tumours, so that the appropriate therapies can be subsequently applied. A number of groups have recently published reports utilizing expression profile data to classify breast cancers into ER+ and ER− categories. In one study, it was found that the expression profiles of ER+ and ER− tumours are ‘remarkably distinct’, supporting previous theories that ER+ and ER− tumours may arise from distinct breast epithelial cell types (3).

Another group has reported the use of supervised learning methodologies on expression data to classify breast tumours by ER subtype (4). One common observation in these studies was that that although the majority of breast tumours could usually be accurately classified into ER+ and ER− subtypes to a high degree of certainty, there always existed a set of ‘low-confidence’ samples that were either misclassified or where the statistical ‘confidence’ of the predictions was marginal. Although it was proposed that these ‘low-confidence’, samples might reflect the effects of population heterogeneity (4), the hypothesis that such ‘low-confidence’ samples might be biologically distinct from their ‘high-confidence counterparts has not been fully explored to date.

SUMMARY OF THE INVENTION

The present inventors considered the possibility that the ‘low confidence’ samples might possess distinct biological characteristics. In order to assess this, they performed a classification analysis using an in-house generated breast cancer expression dataset, and determined that in comparison to the ‘high confidence’ tumours, the ‘low-confidence’ tumours exhibit widespread perturbations in the expression of multiple genes important for ER subtype discrimination. Although initially derived through purely computational means, the distinction between ‘high’ and ‘low’ confidence tumours is clinically meaningful, as ‘low-confidence’ tumours exhibited a significantly worse overall survival (p=0.0003) and shorter time to distant metastasis (p=0.001) than their ‘high-confidence’ counterparts. Such a distinction is currently not discernible by conventional immunohistochemical strategies used to detect ER.

The inventors have surprisingly further determined that high expression levels of the ERBB2 receptor are significantly correlated with breast tumours exhibiting a ‘low confidence’ prediction, and validated this association across three independently-derived breast cancer expression datasets generated from different patient populations/array technologies, and analyzed using different computational methods. The association between ERBB2 expression and the widespread perturbations of ER-discriminator genes observed in the ‘low-confidence’ tumours is intriguing, as ERBB2 activity is known to contribute, in both breast tumours and cell lines, towards the development of resistance to anti-hormonal therapies (5, 6), and to inhibit the transcriptional activity of ER (5, 7).

However, despite being important for ER subtype discrimination, the inventors found that a significant proportion of these ‘perturbed’ genes, are not known to be estrogen responsive, and using a recently described bioinformatics algorithm (DEREF) also demonstrated that these genes do not contain potential estrogen-response elements (ERE's) in their promoters. These results suggest that, in addition to current models where ERBB2 acts primarily by disrupting the transcriptional activity of ER, a significant fraction of ERBB2's effects on breast tumours may involve ER-independent mechanisms of gene activation as well, which may collectively contribute to the clinically aggressive nature of the ‘low-confidence’ breast tumour subtype.

Thus, the present inventors have determined sets of genes (“multigene classifiers”), which may be used to classify a breast tumour sample as a “low confidence” tumour or a “high confidence” tumour. The inventors have determined for the first time that the “low confidence” group of tumours has significant medical implications with regard to prognosis and treatment.

For each of ER+ and ER−, the inventors have provided a number of genes that have altered expression levels between “high confidence” and “low confidence” tumours. These genes are identified in Table 2. The levels of expression of these perturbed genes can be used to discriminate between high confidence and low confidence tumours. A further set of genes, which have distinctive expression levels in low confidence tumours as compared to high confidence tumours, is identified in Table S4. Further sets of genes that have distinctive expression levels in low confidence tumours as compared to high confidence tumours, irrespective of the ER status of the tumour, are identified in Tables A1-A4. The following description will make use of the term “expression profile”. This refers to the expression levels in a sample of a set of genes from a multigene classifier.

The expression levels will generally be represented numerically. The expression profile therefore will generally include a set of numbers, each number representing the expression level of a gene of a multigene classifier. The following description will make use of the term “a plurality of genes”. This term refers to a subset of the genes from a multigene classifier. The subset may correspond to a sub-grouping of the multigene classifier e.g. upregulated genes in ER+ low confidence breast tumours. The content of the plurality of genes may vary across multigene classifiers and, for a particular multigene classifier, across different aspects of the invention. The term may mean all of the genes of a particular multigene classifier or a subset thereof.

Accordingly, at its most general, the present invention provides new diagnostic methods and assays for classifying, using a multigene classifier, a breast tumour sample as a high or low confidence sample. The invention further identifies multigene classifiers for use in classifying breast tumour samples and apparatus comprising a multigene classifier or a plurality of genes therefrom. The multigene classifiers for use in aspects of the invention are shown in Tables S4, 2, A1, A2, A3, and A4.

Table S4 lists the genes that exhibit significant differential transcriptional regulation between high confidence and low confidence tumours when examined on a global scale in each of ER+ and ER− tumours.

In a first aspect, there is provided a method of producing a nucleic acid expression profile for a breast tumour sample comprising the steps of

-   -   (a) isolating expression products from said breast tumour         sample;     -   (b) identifying the expression levels of a plurality of genes         selected from Table S4; and     -   (c) producing from the expression levels an expression profile         for said breast tumour sample.

The tumour sample may be high confidence and/or low confidence. The tumour sample may be an ER+ high confidence breast tumour sample and/or ER+ low confidence breast tumour sample and/or ER− high confidence breast tumour sample and/or ER− low confidence breast tumour sample. Preferably, the ER status of the breast tumour sample is determined. The ER status of the breast tumour sample is preferably determined before step a) of the method. The ER status of the breast tumour sample may be determined using gene expression profiling as described in our co-pending application PCT/GB03/000755.

The genes of Table S4 are shown in subsets. In subset (a) are genes that showed significantly altered expression in ER+ high confidence samples compared to ER+ low confidence tumours. In the first part of Table S4(a) is a group of genes that are upregulated (Table S4(a) ‘upregulated’) in ER+ low confidence tumours compared to ER+ high confidence tumours. The second part of Table S4(a) shows a group of genes that are downregulated (Table S4(a) downregulated) in ER+ low confidence tumours compared to ER+ high confidence tumours.

In part (b) of Table S4 are genes that show upregulated expression in ER− low confidence samples compared to ER− high confidence tumours.

The expression profile of the individual genes of the multigene classifier will differ slightly between independent samples. However, the inventors have realised that the expression profile of genes of the multigene classifiers provide a characteristic pattern of expression that recognisably differs between high confidence and low confidence tumours.

By creating a number of expression profiles of a multigene classifier from a number of known high and low confidence samples it is possible to create a library of profiles for both high confidence and low confidence samples. The greater the number of expression profiles, the easier it is to create a reliable characteristic expression profile standard (i.e. including statistical variation) that can be used as a control in a diagnostic assay. Thus, a standard profile may be one that is derived from a plurality of individual expression profiles and derived within statistical variation to represent either the high confidence or low confidence sample profile.

Thus, the method according to the first aspect of the invention may comprise the steps of

-   -   (a) isolating expression products from a breast tumour sample;     -   (b) contacting said expression products with a plurality of         binding members capable of specifically and independently         binding to expression products of a plurality of genes selected         from Table S4, so as to create a first expression profile of a         tumour sample from the expression levels of said plurality of         genes;     -   (c) comparing the expression profile with an expression profile         characteristic of a high confidence tumour and/or a low         confidence breast tumour.

The expression levels of the plurality of genes are assessed to produce the expression profile. The expression levels may be assessed absolutely i.e. a measurement of the amount of an expressed product. The expression levels may be assessed relatively i.e. expression compared to some other factor, such as, but not limited to expression of another gene, or a mean/median/mode of expression of a group of genes (preferably a group of genes not included in the multigene classifier used in the method) in the sample or across a group of samples. For example, expression of a gene may be measured as a multiple or fraction of the average expression of a plurality of genes in the sample. The expression is preferably denoted as positive or negative to indicate an increase or decrease in expression relative to the average value.

The prediction strength is preferably measured using a statistical and/or probabilistic model. The model comprises Weighted Voting (WV) and/or Support Vector Machines. The prediction strength may be determined using Weighted Voting and Leave One Out Cross Validation (see examples). Low confidence may mean a prediction strength of magnitude less than, or equal to, 0.4, when calculated using 2-colour cDNA microarrays, for example those used for assessing the Stanford data set. Preferably, the range of prediction strength for a low confidence tumour is ≧−0.4, and preferably ≦0.4. The prediction strength may be ≧−0.35, and preferably ≦0.35 for a low confidence tumour. The prediction strength may be ≧−0.3, and preferably ≦0.3 for a low confidence tumour.

Preferably, high confidence samples have a prediction strength of magnitude greater than 0.4. Preferably, the prediction strength of high confidence tumours is ≧0.4, and preferably ≦−0.4.

However, the cut-off value of prediction strength for high/low confidence tumours may vary on the dataset and/or array technology used. For example, in the Rosetta data set, assessed using 2 color oligonucleotide microarrays, high confidence tumours are those with a prediction strength of magnitude greater than 0.7. The high confidence samples preferably have a prediction strength of magnitude greater than 0.7. Therefore, the prediction strength may be ≧−0.7, and preferably ≦0.7 for a low confidence tumour. The prediction strength may be ≧−0.6, and preferably ≦0.6 for a low confidence tumour. The prediction strength may be ≧−0.5, and preferably ≦0.5 for a low confidence tumour. More preferably, the range of prediction strength for a low confidence tumour is ≧−0.4, and preferably ≦0.4.

When the prediction strengths in a breast tumour population are compared in both Stanford and Rosetta data sets, the boundaries between high and low confidence tumours are identifiable as the points at which the prediction strength of tumours in the data set begin to demonstrate qualitatively reduced prediction strengths (the ‘cliff-points’) from the majority of the prediction strengths in the tumour population. Although each dataset was analyzed independently, the proportions of low-confidence tumours for the independent Rosetta and Stanford data sets are similar.

A low-confidence tumour may therefore fall within the lowest 20% of the ER prediction strengths in a breast tumour population, and more preferably the lowest 15-19% of ER prediction strengths. A breast tumour population preferably comprises a minimum data set of at least 25, more preferably at least 25-30 tumours, more preferably at least 30 tumours, more preferably at least 50 tumours, more preferably at least 80 tumours and most preferably around 80-100 tumours.

The expression products are preferably mRNA, or cDNA made from said mRNA, or cDNA. Alternatively, the expression product could be an expressed polypeptide. Identification of the expression profile is preferably carried out using binding members capable of specifically identifying the expression products of the plurality of genes identified in Table S4. For example, if the expression products are cDNA then the binding members will be nucleic acid probes capable of specifically hybridising to the cDNA.

Preferably, either the expression product or the binding member will be labelled so that binding of the two components can be detected. The label is preferably chosen so as to be able to detect the relative levels/quantity and/or absolute levels/quantity of the expressed product so as to determine the expression profile based on the up-regulation or down-regulation of the individual genes of the multigene classifier. Generally, the binding members should be capable of not only detecting the presence of an expression product but its relative abundance (i.e. the amount of product available).

There are, however, a number of newer technologies that have recently emerged that utilize ‘label-free’ techniques for quantitation, for example, those produced by Xagros. The expression product and/or the binding member may be unlabelled. Binding to the binding member may be detected and/or quantitated by measuring the change in electrical resistance as a result of two primers docking onto a target expressed product and subsequent extension by polymerase.

The determination of the nucleic acid expression profile may be carried out within certain previously set parameters, to avoid false positives and false negatives. A computer may be used to determine the nucleic acid expression profile.

The computer may then be able to provide an expression profile standard characteristic of a low confidence or high confidence breast cell as discussed above. The determined expression profiles may then be used to classify breast tissue samples as a way of diagnosis.

Thus, in a second aspect of the invention, there is provided an expression profile database comprising a plurality of gene expression profiles of high confidence and/or low confidence breast tumour samples wherein each gene expression profile is derived from a plurality of genes selected from Table S4, and wherein the database is retrievably held on a data carrier. Preferably, the expression profiles making up the database are produced by the method according to the first aspect.

With the knowledge of the multigene classifiers, it is possible to devise many methods for determining the expression pattern or profile of the genes in a particular test sample. For example, the expressed nucleic acid (RNA, mRNA) can be isolated from the sample using standard molecular biological techniques. The expressed nucleic acid sequences corresponding to the said plurality of genes from the genetic identifiers given in Table S4 can then be amplified using nucleic acid primers specific for the expressed sequences in a PCR. If the isolated expressed nucleic acid is mRNA, this can be converted into cDNA for the PCR reaction using standard methods.

The primers may conveniently introduce a label into the amplified nucleic acid so that it may be identified. Ideally, the label is able to indicate the relative quantity or proportion of nucleic acid sequences present after the amplification event, reflecting the relative quantity or proportion present in the original test sample. For example, if the label is fluorescent or radioactive, the intensity of the signal will indicate the relative quantity/proportion or even the absolute quantity, of the expressed sequences. The relative quantities or proportions of the expression products of each of the genetic identifiers will establish a particular expression profile for the test sample. By comparing this profile with known profiles or standard expression profiles, it is possible to determine whether the test sample was from normal breast tissue or malignant breast tissue. The primers and/or amplified nucleic acid may be unlabelled, as discussed above.

Alternatively, the expression pattern or profile can be determined using binding members capable of binding to the expression products of the genetic identifiers, e.g. mRNA, corresponding cDNA or expressed polypeptide. By labelling either the expression product or the binding member it is possible to identify the relative quantities or proportions of the expression products and determine the expression profile of the genetic identifiers. In this way the sample can be classified high confidence or low confidence by comparison of the expression profile with known profiles or standards. The binding members may be complementary nucleic acid sequences or specific antibodies. Microarray assays using such binding members are discussed in more detail below.

In a third aspect of the present invention, there is provided a method for classifying a breast tumour sample as low confidence or high confidence, the method comprising providing the expression profile of said breast tumour sample, wherein the expression profile comprises the expression level of a plurality of genes from Table S4, and classifying the tumour as a high or low confidence tumour based on the expression profile.

The method of the third aspect of the invention may comprise the steps of:

-   -   (a) obtaining expression products from a breast tumour sample         obtained from a patient;     -   (b) determining the expression levels of a plurality of genes         identified in Table S4 by contacting said expression products         with binding members, each binding member being capable of         specifically binding to an expression product of the plurality         of genes; and     -   (c) identifying the presence of a low confidence breast tumour         in said patient based on the expression levels.

Preferably the method further includes the step of determining the ER status of the tumour, preferably before providing the expression profile of the tumour.

The step of determining the presence of a low confidence breast tumour may be carried out by a computer which is able to compare the binding profile of the expression products from the breast tumour sample under test with a database of other previously obtained profiles and/or a previously determined “standard” profile which is characteristic of the presence of low confidence tumour. The computer may be programmed to report the statistical similarity between the profile under test and the standard profiles so that a classification may be made.

The step of classifying the breast tumour sample may comprise the use of statistical and/or probabilistic techniques, such as weighted Voting (WV) (13), a supervised learning technique. In WV, binary classifications may be performed. The expression level of genes in the multigene classifier in the breast tumour sample is compared to the mean average level of expression of that gene across the different classes. The mean average may, for example, be calculated from expression profiles that have an assigned class, e.g. database of expression profiles of high and/or low confidence samples. Preferably, the profiles have an assigned ER status.

The difference between the expression level and the mean average gene expression across the classes is weighted and corresponds to a ‘vote’ for that gene for a particular class. For a particular tumour, the votes for all the genes are summed together for each class to create totals for each class. The tumour is assigned to the class having the highest number of votes. The margin of victory of the winning class can then be expressed as prediction strength.

The difference in expression level is weighted using a formula that includes mean and standard deviations of expression levels of the genes in each of the two classes. Generally, the mean and standard deviations for each class are calculated from expression profiles that have, or represent, a particular class of tumour e.g. high confidence and low confidence.

Additionally, or alternatively, step (c) may comprise the use of hierarchical clustering, particularly if the tumour sample has been assessed using a different array technology from the one used to assess the expression profiles with assigned classes, or standard profile(s) to which the sample expression profile is compared. The result of step (c) may be validated using an established leave-one-out cross validation (LOOCV) assay (see examples). Step (c) may be performed using a computer.

In Hierarchical Clustering, each expression profile can be represented as a vector that consists of n genes where (g1, g2 . . . gn) represent the expression levels of the genes. Each vector is then compared with every other profile in the analysis, and the two vectors with the highest correlation to one another are paired together until as many profiles as possible in the analysis have been paired up.

There are many ways known in the art to calculate the correlation, such as the Pearson's correlation coefficient (28). In the next step, a composite vector is then derived from each pair (in average-linkage clustering this is usually the average of both profiles), and then the process of pairing is repeated. This continues until no more pairings are possible. The process is ‘hierarchical’ as one starts from the bottom (individual profiles) and builds up. In the present invention, individual profiles build up to preferably two composite vectors, each vector representing a class (i.e. high confidence and low confidence). For a new sample of unknown class, the sample is clustered with the standard profiles/samples. The class of ‘unknown’ sample will be determined based on which cluster/vector it belongs to at the end of the iterative rounds of pairing.

The present invention therefore provides in one embodiment a method to identify an aggressive breast tumour in a patient, for example by comparing the said tumour's expression profile to a profile that is characteristic of tumour class, preferably by comparing the tumour's expression profile to a profile characteristic of a high confidence and/or of a low confidence tumour. The method may further comprise the step of assigning a poor prognosis to the patient where the tumour has an expression profile characteristic of a low confidence tumour expression profile.

The prognosis may affect the course of treatment of the patient. After identifying the low confidence tumour, the patient may be treated using aggressive techniques to treat the low confidence tumour.

A poor prognosis includes significantly worse overall survival rate of the patient and/or significantly shorter time to distant metastasis than a patient with a high confidence tumour.

As mentioned above, the present inventors have identified several key genes which have a different expression pattern in low confidence breast tumours as opposed to high confidence breast tumours, i.e. they are able to distinguish high and low confidence classes of breast tumour.

The multigene classifier may comprise genes that are given in Table S4. By determining an expression profile of a test sample and comparing the expression profile to expression profiles characteristic of low and/or high confidence breast tumours (and/or analysing the expression profile using techniques such as Weighted Voting), it is possible to classify the sample as a low confidence or high confidence tumour, e.g. an increase or decrease in their expression, relative to a standard pattern or profile seen in high confidence samples.

The plurality of genes may be the genes of Table S4(a) and/or Table S4(b), or a subset of the genes of Table S4(a) and/or a subset of the genes of Table S4(b).

The plurality of genes may include at least 10, 20, 30, 40, 50, 60, 70, 80 or all of the genes of Table S4(a).

The plurality of genes may be all, or substantially all, of the upregulated and/or downregulated genes from Table S4(a).

The plurality of genes may comprise, or consist of, about thirty, or about twenty, or about ten, or about five of the upregulated genes from Table S4a. The plurality of genes may comprise, or consist of, about thirty, or about twenty, or about ten, or about five of the downregulated genes from Table S4a.

Preferably, the plurality of genes comprises, or consists of, about eighty, or about seventy, or about sixty, or about fifty, or about forty, or about thirty or about twenty or about ten genes from Table S4(a). The plurality of genes may comprise, or consist of, about fifty, or about forty, or about thirty or about twenty or about ten, or about five, of the upregulated genes from Table S4(a).

Genes from Table S4(a) are preferably selected from the upper portion of the upregulated group of genes and/or the upper portion of the downregulated group of genes. The upper portion is preferably the upper half of the table or group, as the genes are ranked in order of significance in each group. Genes that show the most differential expression between high confidence and low confidence tumours appear in the upper portion in each group of Table S4(a), whereas those genes that are less differentially expressed appear in the lower portion.

The plurality of genes may include no more than eighty, or seventy, or sixty, or fifty, or forty, or thirty, or twenty, or ten, or five genes of Table S4(a).

The plurality of genes may comprise, or consist essentially of, five to thirty genes of Table S4(a) upregulated and/or of Table S4(a) downregulated. The plurality of genes may comprise, or consist essentially of, ten to thirty genes of Table S4(a) upregulated and/or of Table S4(a) downregulated.

The plurality of genes may comprise, or consist essentially of, ten to twenty-genes of Table S4(a) upregulated and/or of Table S4(a) downregulated, or twenty to thirty genes of Table S4(a) upregulated and/or of Table S4(a) downregulated. The plurality of genes may comprise, or consist essentially of, five to forty genes or five to fifty genes of Table S4(a) upregulated.

The plurality of genes, which may be about ten genes, may be selected from the first about forty, or about thirty, or about twenty genes of Table S4(a) upregulated and/or of Table S4(a) downregulated. The about ten genes may be selected from the first about fifteen genes of Table S4(a) upregulated and/or of Table S4(a) downregulated. The about ten genes may be the first ten genes of Table S4(a) upregulated or of Table S4(a) downregulated. The plurality of genes, which may be about ten genes, may be selected from the first about fifty, or about forty, genes of Table S4(a) upregulated.

Preferably, the plurality of genes comprises about ten to twenty genes of the first about thirty genes of Table S4(a) upregulated and/or of Table S4(a) downregulated.

The plurality of genes may comprise, or consist of, about thirty or about twenty or about ten genes selected from the group consisting of the first about forty, or about thirty or about twenty or about ten genes of Table S4(a) upregulated and the first about thirty or about twenty or about ten genes of Table S4(a) downregulated. The plurality of genes may comprise, or consist of, about ten or about fifteen or about twenty genes selected from the group consisting of the first about ten or fifteen genes of Table S4(a) upregulated and the first about ten or fifteen or about twenty genes of Table S4(a) downregulated.

The plurality of genes may be all, or substantially all, of the genes from Table S4(b). The plurality of genes may be all, or substantially all, of the genes from Table S4(b).

The plurality of genes may include at least 10, 20, 30, 40, 50, or all, of the genes of Table S4(b).

The plurality of genes may comprise, or consist of, about fifty, or about forty, or about thirty, or about twenty, or about ten, or about five of the genes from Table S4(b).

Genes from Table S4(b) are preferably selected from the upper portion of the Table. The upper portion is preferably the upper half of the table, as the genes are ranked in order of significance in each group. Genes that show the most differential expression between high confidence and low confidence tumours appear in the upper portion of Table S4(b), whereas those genes that are less differentially expressed appear in the lower portion.

The plurality of genes may include no more than fifty, or forty, or thirty, or twenty, or ten, or five genes of Table S4(b).

The plurality of genes may comprise, or consist essentially of, five to fifty genes of Table S4(b). The plurality of genes may comprise, or consist essentially of, ten to forty genes of Table S4(b). The plurality of genes may comprise, or consist essentially of, ten to thirty genes of Table S4(b). The plurality of genes may comprise, or consist essentially of, ten to twenty genes of Table S4(b), or twenty to thirty genes of Table S4(b).

The plurality of genes, preferably about thirty or about twenty or about ten genes, may be selected from the first about forty, or about thirty, or about twenty, genes of Table S4(b). About ten genes may be selected from the first about fifteen or twenty genes of Table S4b. The about ten genes may be the first ten genes of Table S4b.

Preferably, the plurality of genes comprises about ten to twenty genes of the first about thirty genes of Table S4(b).

As discussed previously, those skilled in the art will appreciate that fewer of the most significant genes are required to produce a characteristic expression profile compared to the number of the least significant genes required to produce a characteristic expression profile.

The number and choice of said plurality of genes are selected so as to provide an expression signature that is capable of distinguishing between high confidence and low confidence tumours.

Preferably, the plurality of genes includes a mixture of upregulated and downregulated genes from Table S4(a) and/or Table S4(b).

The step of classifying the tumour may comprise assessing genes that have been upregulated in a low confidence tumour compared to a high confidence tumour.

Additionally or alternatively, step (c) may comprise assessing genes that have been downregulated in a low confidence tumour compared to a high confidence tumour.

Genes that make up a further multigene classifier are shown in Table 2. The first, second and third aspects of the invention apply mutatis mutandis to Table 2 i.e. the plurality of genes may be from Table 2. The preferred embodiments and optional features of the first, second and third aspects of the invention apply mutatis mutandis to Table 2.

In a fourth aspect therefore, there is provided a method of producing a nucleic acid expression profile for a breast tumour sample comprising the steps of

-   -   (a) isolating expression products from said breast tumour         sample;     -   (b) identifying the expression levels of a plurality of genes         from Table 2; and     -   (c) producing from the expression levels an expression profile.

The breast tumour sample may be any class of breast tumour, as discussed for the first aspect of the invention. Preferably, the ER status of the breast tumour sample is determined, preferably before step (a).

In a fifth aspect of the invention, there is provided an expression profile database comprising a plurality of gene expression profiles of high confidence and/or low confidence breast samples wherein each expression profile is derived from a plurality of genes from Table 2, and wherein the database is retrievably held on a data carrier. Preferably, the expression profiles making up the database are produced by the method according to the fourth aspect.

The genes of Table 2 provide an alternative multigene classifier.

In a sixth aspect of the invention, there is provided a method for classifying a breast tumour sample as either low confidence or high confidence, the method comprising providing the expression profile of said sample, wherein the expression profile comprises the expression levels of a plurality of genes from Table 2, and classifying the tumour as a high or low confidence tumour based on the expression profile.

The sixth aspect of the invention may comprise the steps of:

-   -   (a) obtaining expression products from a breast tumour sample         obtained from a patient;     -   (b) determining the expression levels of a plurality of genes         identified in Table 2 by contacting said expression products         with binding members, each binding member being capable of         specifically binding to an expression product of the plurality         of genes; and     -   (c) identifying the presence of a low confidence breast tumour         in said patient based on the expression levels.

Step (c) may comprise comparing the binding profile to the profile characteristic of a low confidence tumour. The low confidence tumour may be ER+ or ER−. Step (c) may comprise the use of a statistical technique, such as Weighted Voting and/or Support Vector Machines (SVM).

The plurality of genes may comprise, or consist of, all, or substantially all, of the genes from Table 2, or all, or substantially all of the genes from either Table 2a or Table 2b.

The plurality of genes may include at least 10, 20, 30, 40, 50, 60, 70, 80, 90 or all of the genes of Table 2.

Preferably, the plurality of genes comprises, or consists of, about fifty or about forty or about thirty or about twenty or about ten genes from Table 2a and/or from Table 2b. Genes from Table 2 are preferably selected from the upper portion, preferably the upper half, of Table 2a and/or of Table 2b, as the genes are ranked in order of significance in each of Tables 2a and 2b. Genes that show the most perturbation between high confidence and low confidence tumours appear in the upper portion in each of Table 2a and Table 2b, whereas those genes that are less perturbed appear in the lower portion.

Those skilled in the art will appreciate that fewer of the most significant genes are required to produce an expression profile characteristic of a low and/or high confidence breast tumour compared to the number of the least significant genes required to produce a said characteristic expression profile. For example, fewer genes are required from the upper half of Table 2a than genes selected from the lower half of the Table.

The number and choice of said plurality of genes are selected so as to provide an expression signature that is capable of distinguishing between high confidence and low confidence tumours.

The plurality of genes may include no more than fifty genes of Table 2a and/or of Table 2b. The plurality of genes may include no more than forty genes of Table 2a and/or of Table 2b. The plurality of genes may include no more than thirty genes of Table 2a and/or of Table 2b. The plurality of genes may include no more than twenty genes of Table 2a and/or of Table 2b. The plurality of genes may include no more than ten genes of Table 2a and/or of Table 2b. The plurality of genes may include no more than five genes of Table 2a and/or of Table 2b.

The plurality of genes may comprise, or consist essentially of, five to fifty genes of Table 2a and/or of Table 2b. The plurality of genes may comprise, or consist essentially of, ten to forty genes of Table 2a and/or of Table 2b. The plurality of genes may comprise, or consist essentially of, ten to thirty genes of Table 2a and/or of Table 2b. The plurality of genes may comprise, or consist essentially of, ten to twenty genes of Table 2a and/or of Table 2b, or twenty to thirty genes of Table 2a and/or of Table 2b.

The said genes, preferably about ten genes, may be selected from the first about forty, or about thirty, or about twenty genes of Table 2a. The about ten genes may be selected from the first about fifteen genes of Table 2a. The about ten genes may be the first ten genes of Table 2a. The said genes, preferably about ten genes, may be selected from the first about forty, or about thirty, or about twenty, genes of Table 2b. The about ten genes may be selected from the first about fifteen genes of Table 2b. The about ten genes may be first ten genes of Table 2b.

The said genes, preferably about ten to twenty genes, are preferably selected from the first about thirty genes of Table 2a and/or Table 2b.

The plurality of genes may comprise, or consist of, about thirty or about twenty or about ten genes selected from the group consisting of the first about twenty genes of Table 2a and the first about twenty genes of Table 2b. The plurality of genes may comprise, or consist of, about ten or about fifteen or about twenty genes selected from the group consisting of the first about ten genes of Table 2a and the first about ten genes of Table 2b.

The methods of the invention preferably further comprise the preclassification step of determining ER+ or ER− status. The ER status may be determined by immunohistochemistry (e.g. using antibodies to ER) or by using a probabilistic/statistical model that is adapted to assess gene expression profiles.

The inventors have conducted further analyses and identified further multi-gene classifiers for discriminating between high and low confidence tumours. The objective of these analyses was to identify an optimal set of genes that could be used to classify “high” and “low-confidence” tumours regardless of their ER status. A series of three independent analytical methods (Significance Analysis of Microarrays, Gene Ranking, and The Wilcoxon Test) were used to identify genes that were differentially expressed between the two groups (LC and HC). The results of the analyses are the further multigene classifiers shown in Tables A1, A2, A3 and A4.

In Table A1, there are 88 genes that can be used to discriminate between high and low confidence tumours. Table A1 genes were identified using SAM (Significance Analysis of Microarrays). 86 of the genes are upregulated in low confidence tumours, whilst 2 of the genes are upregulated in high confidence tumours.

In Table A2, there are 251 genes that can be used to discriminate between high and low confidence tumours. Table A2 genes were identified using GR (Gene Ranking) by SVM.

In Table A3, there are 38 genes that can be used to discriminate between high and low confidence tumours. Table A3 genes were identified using a WT (Wilcoxon Test) at a P-value of <0.05 and a >=2-fold change cutoff.

In Table A4, there are 13 common genes (i.e. genes that are found in Tables A1, A2, A3). These 13 ‘common genes’ are robust significant markers and can achieve comparable discriminatory performance as other ‘complete’ marker sets.

In a seventh aspect therefore, there is provided a method of producing a nucleic acid expression profile for a breast tumour sample comprising the steps of:

-   -   (a) isolating expression products from said breast tumour         sample;     -   (b) identifying the expression levels of a plurality of genes         from Table A4 and/or Table A1 and/or Table A2 and/or Table A3;         and     -   (c) producing from the expression levels an expression profile.

The breast tumour sample may be any class of breast tumour, as discussed for the first aspect of the invention.

In an eighth aspect of the invention, there is provided an expression profile database comprising a plurality of gene expression profiles of high confidence and/or low confidence breast samples wherein each expression profile is derived from a plurality of genes from Table A4 and/or Table A1 and/or Table A2 and/or Table A3, and wherein the database is retrievably held on a data carrier. Preferably, the expression profiles making up the database are produced by the method according to the seventh aspect.

In a ninth aspect of the invention, there is provided a method for classifying a breast tumour sample as either low confidence or high confidence, the method comprising providing the expression profile of said sample, wherein the expression profile comprises the expression levels of a plurality of genes from Table A4 and/or Table A1 and/or Table A2 and/or Table A3, and classifying the tumour as a high or low confidence tumour based on the expression profile.

The ninth aspect of the invention may comprise the steps of:

-   -   (a) obtaining expression products from a breast tumour sample         obtained from a patient;     -   (b) determining the expression levels of a plurality of genes         identified in Table A4 and/or Table A1 and/or Table A2 and/or         Table A3 by contacting said expression products with binding         members, each binding member being capable of specifically         binding to an expression product of the plurality of genes; and     -   (c) identifying the presence of a low confidence breast tumour         in said patient based on the expression levels.

Step (c) may comprise deriving comparing the expression levels to a profile characteristic of a low and/or high confidence tumour. The low confidence tumour may be ER+ or ER−. Step (c) may comprise the use of a statistical technique, such as Weighted Voting and/or Support Vector Machines (SVM).

The plurality of genes preferably comprises, or consists essentially of, substantially all of the genes of Table A4. Further genes from each of Tables A1, A2 and A3 may be included, although, independently, the plurality of genes may be from any one or more of Tables A1, A2, and A3. The plurality of genes does not necessarily need to include the genes of Table A4.

The first, second and third aspects of the invention therefore apply mutatis mutandis to each one of Tables A1, A2 and A3, above i.e. in each aspect of the invention, the plurality of genes may be from any one or more of Table A1 and Table A2 and Table A3. The embodiments and preferred/optional features of the first, second and third aspects of the invention apply mutatis mutandis to Tables A1, A2, A3 and A4.

The plurality of genes may include at least 10, 20, 30, 40, 50, 60, 70, 80, or all of the genes of Table A1.

The plurality of genes may be all, or substantially all, of the ‘upregulated in low confidence’ and/or ‘upregulated in high confidence genes’ from Table A1. The plurality of genes may comprise, or consist of, about eighty, or about seventy, or about sixty, or about fifty, or about forty, or about thirty, or about twenty, or about ten, or about five of the ‘upregulated in low confidence’ genes from Table A1. The plurality of genes may include either one or both of the ‘upregulated in high confidence’ genes from Table A1.

Genes from Table A1 are preferably selected from the upper portion of the ‘upregulated in low confidence’ group of genes. The upper portion is preferably the upper half of the Table, as the genes are ranked in order of significance. Genes that show the most differential expression between high confidence and low confidence tumours appear in the upper portion of Table A1, whereas those genes that are less differentially expressed appear in the lower portion.

The plurality of genes may include no more than eighty, or seventy, or sixty, or fifty, or forty, or thirty, or twenty, or ten, or five genes of Table A1.

The plurality of genes may comprise, or consist essentially of, five to seventy genes of Table A1. The plurality of genes may comprise, or consist essentially of, ten to sixty genes of Table A1. The plurality of genes may comprise, or consist essentially of, ten to fifty, or ten to forty, or ten to thirty genes of Table A1.

The plurality of genes, which may be about ten to fifteen genes, may be selected from the first about forty, or about thirty, or about twenty genes of Table A1. Preferably, the plurality of genes comprises about ten to twenty genes of the first about thirty genes of Table A1.

The plurality of genes may include at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150 or all of the genes of Table A2.

The plurality of genes may include no more than 250, or 240, or 230, or 220, or 210, or 200, or 190, or 180, or 170, or 160, or 150, or 140, or 130, or 120, or 110, or 100, or 90, or 80, or 70, or 60, or 50, or 40, or 30, or 20, or 10, or 5 genes of Table A2.

The plurality of genes may comprise, or consist essentially of, 5 to 200 genes of Table A2. The plurality of genes may comprise, or consist essentially of, 10 to 150 genes of Table A2. The plurality of genes may comprise, or consist essentially of, 10 to 100, or 10 to 70, or 10 to 50 genes of Table A2.

The plurality of genes, which may be about ten to fifteen genes, may be selected from the first about fifty, or about forty, or about thirty, or about twenty genes of Table A2. Preferably, the plurality of genes comprises about ten to twenty genes of the first about thirty genes of Table A2.

The plurality of genes may include at least 10, 20, 30, 35, or all of the genes of Table A3.

The plurality of genes may include no more than 35, or 30, or 20, or 10, or 5 genes of Table A3.

The plurality of genes may comprise, or consist essentially of, 5 to 35 genes of Table A3. The plurality of genes may comprise, or consist essentially of, 10 to 30 genes of Table A3. The plurality of genes may comprise, or consist essentially of, 10 to 20, or 20 to 30 genes of Table A3.

The plurality of genes, which may be about ten to fifteen genes, may be selected from the first thirty, or about twenty genes of Table A3. Preferably, the plurality of genes comprises about ten to twenty genes of the first about thirty genes of Table A3.

The plurality of genes may include at least 5, 10, 15 or all of the genes of Table A4.

The plurality of genes may include no more than 10, or 8, or 6, or 5 genes of Table A4.

The plurality of genes may comprise, or consist essentially of, 5 to 13 genes of Table A4. The plurality of genes may comprise, or consist essentially of, 10 to 13 genes of Table A4.

In the context of the plurality of genes, the term ‘about’ means the number of genes stated plus or minus the greater of: 10% of the number of genes stated or one gene.

As before, the expression product may be a transcribed nucleic acid sequence or the expressed polypeptide. The transcribed nucleic acid sequence may be RNA or mRNA. The expression product may also be cDNA produced from said mRNA. The expression product may be cRNA.

The binding member may a complementary nucleic acid sequence which is capable of specifically binding to the transcribed nucleic acid under suitable hybridisation conditions. Typically, cDNA or oligonucleotide sequences are used.

Where the expression product is the expressed protein, the binding member is preferably an antibody, or molecule comprising an antibody binding domain, specific for said expressed polypeptide.

The binding member may be labelled for detection purposes using standard procedures known in the art. Alternatively, the expression products may be labelled following isolation from the sample under test. A preferred means of detection is using a fluorescent label which can be detected by a light meter. Alternative means of detection include electrical signalling. For example, the Motorola e-sensor system has two probes, a “capture probe” which is freely floating, and a “signalling probe” which is attached to a solid surface which doubles as an electrode surface. Both probes function as binding members to the expression product. When binding occurs, both probes are brought into close proximity with each other resulting in the creation of an electrical signal which can be detected.

As discussed above, the binding members may be oligonucleotide primers for use in a PCR (e.g. multi-plexed PCR) to specifically amplify the number of expressed products of the genetic identifiers. The products would then be analysed on a gel. However, preferably, the binding member a single nucleic acid probe or antibody fixed to a solid support. The expression products may then be passed over the solid support, thereby bringing them into contact with the binding member. The solid support may be a glass surface, e.g. a microscope slide; beads (Lynx); or fibre-optics. In the case of beads, each binding member may be fixed to an individual bead and they are then contacted with the expression products in solution.

Various methods exist in the art for determining expression profiles for particular gene sets and these can be applied to the present invention. For example, bead-based approaches (Lynx) or molecular bar-codes (Surromed) are known techniques. In these cases, each binding member is attached to a bead or “bar-code” that is individually readable and free-floating to ease contact with the expression products. The binding of the binding members to the expression products (targets) is achieved in solution, after which the tagged beads or bar-codes are passed through a device (e.g. a flow-cytometer) and read.

A further known method of determining expression profiles is instrumentation developed by Illumina, namely, fibre-optics. In this case, each binding member is attached to a specific “address” at the end of a fibre-optic cable. Binding of the expression product to the binding member may induce a fluorescent change which is readable by a device at the other end of the fibre-optic cable.

The present inventors have successfully used a nucleic acid microarray comprising a plurality of nucleic acid sequences fixed to a solid support. By passing nucleic acid sequences representing expressed genes e.g. cDNA, over the microarray, they were able to create an binding profile characteristic of the expression products from tumour samples and normal cells derived from breast tissue.

The present invention further provides apparatus, preferably a microarray, for classifying a breast tumour sample comprising a plurality of binding members attached to a solid support, preferably nucleic acid sequences, each binding member being capable of specifically binding to an expression product of a gene from any one or more of the group of multigene classifiers: Table S4, Table 2, Table A1, Table A2, Table A3 and Table A4. Preferably the apparatus comprises, or consists essentially of, binding members capable of binding to expression products of a plurality of genes, as previously defined for each of the said multigene classifiers (see above). The apparatus may comprise, or consist essentially of, binding members capable of binding to expression products of a plurality of genes from each of the multigene classifiers, or of a plurality of genes from one or more of the multigene classifiers.

The apparatus may include binding members capable of specifically binding to expression products from at least 5 genes, more preferably, at least 10 genes or at least 15 genes from a said multigene classifier or from a subset of a said multi-gene classifier. A subset of a said multi-gene classifier may be, for example, genes from ER+/Low vs. ER+/High in Table 2, or genes from the upregulated group in ER+/Low from Table S4(a). In a most preferred embodiment, the solid support will house binding members being capable of specifically and independently binding to expression products of all genes identified in Table A4.

The apparatus preferably includes binding members capable of specifically binding to expression products from a multigene classifier, or to a plurality of genes thereof, and may include binding members capable of specifically binding to expression products of no more than 14396 of the genes on the U133A microarray. The apparatus may include binding members capable of specifically binding to expression products of no more than 90% of the genes on the U133A microarray. The apparatus may include binding members capable of specifically binding to expression products of no more than 80% or 70% or 50% or 40% or 30% or 20% or 10% or 5% of the genes on the U133A microarray.

Additionally or alternatively, the solid support may house binding members for no more than 14000, no more than 10000, no more than 5000, no more than 3000, no more than 1000, no more than 500, or no more than 400, or no more than 300, or no more than 200, or no more than 100, or no more than 90, or no more than 80, or no more than 70, or no more than 60, or no more than 50, or no more than 40, or no more than 30, or no more than 20, or no more than 10, or no more than 5 different genes.

Typically, high density nucleic acid sequences, usually cDNA or oligonucleotides, are fixed onto very small, discrete areas or spots of a solid support. The solid support is often a microscopic glass side or a membrane filter, coated with a substrate (or chips). The nucleic acid sequences are delivered (or printed), usually by a robotic system, onto the coated solid support and then immobilized or fixed to the support.

In a preferred embodiment, the expression products derived from the sample are labelled, typically using a fluorescent label, and then contacted with the immobilized nucleic acid sequences. Following hybridization, the fluorescent markers are detected using a detector, such as a high resolution laser scanner. In an alternative method, the expression products could be tagged with a non-fluorescent label, e.g. biotin. After hybridisation, the microarray could then be ‘stained’ with a fluorescent dye that binds/bonds to the first non-fluorescent label (e.g. fluorescently labelled strepavidin, which binds to biotin).

A binding profile indicating a pattern of gene expression (expression pattern or profile) is obtained by analysing the signal emitted from each discrete spot with digital imaging software. The pattern of gene expression of the experimental sample can then be compared with that of a control (i.e. an expression profile from a high confidence or low confidence sample) for differential analysis.

As mentioned above, the control or standard, may be one or more expression profiles previously judged to be characteristic of normal or malignant cells. These one or more expression profiles may be retrievable stored on a data carrier as part of a database. This is discussed above. However, it is also possible to introduce a control into the assay procedure. In other words, the test sample may be “spiked” with one or more “synthetic tumour” or “synthetic normal” expression products which can act as controls to be compared with the expression levels of the genetic identifiers in the test sample.

Most microarrays utilize either one or two fluorophores. For two-colour arrays, the most commonly used fluorophores are Cy3 (green channel excitation) and Cy5 (red channel excitation). The object of the microarray image analysis is to extract hybridization signals from each expression product. For one-color arrays, signals are measured as absolute intensities for a given target (essentially for arrays hybridized to a single sample). For two-colour arrays, signals are measured as ratios of two expression products, (e.g. sample and control (controls are otherwise known as a ‘reference’)) with different fluorescent labels.

The apparatus (e.g. microarray) in accordance with the present invention preferably comprises a plurality of discrete spots, each spot containing one or more oligonucleotides and each spot representing a different binding member for an expression product of a gene selected from a said multigene classifier. In one embodiment, the microarray will contain spots for each of the genes provided in one or more of the multigene classifiers. Each spot will comprise a plurality of identical oligonucleotides each capable of binding to an expression product, e.g. mRNA or cDNA, of the gene of Table S4 it is representing.

In a still further aspect of the present invention, there is provided a kit for classifying a breast tumour sample as high confidence or low confidence, said kit comprising binding members, each binding member being capable of specifically binding to an expression product of a plurality of genes identified in a said multigene classifier, and a detection reagent.

The genes of the multigene classifiers are listed with their Unigene accession numbers (corresponding to build 160 of Unigene). The sequence of each gene can therefore be retrieved from the Unigene database. Furthermore, for certain of the genes, Affymetrix (www.affymetrix.com) provide examples of probe sets, including the sequences of the probes, (i.e. binding members in the form of oligonucleotide sequences) which are capable of detecting expression of the gene when used on a solid support. The probe details are accessible from the U133 section of the Affymetrix website using the Unigene ID of the target gene.

If, in the future, one of the Unigene ID's listed in the table were to be merged into a new ID, or split into two or more ID's (e.g. in a new build of the database) or deleted altogether, the sequence of the gene, as intended by the present inventors, is retrievable by accessing build 160 of Unigene.

Preferably, the one or more binding members (antibody binding domains or nucleic acid sequences e.g. oligonucleotides) in the kit are fixed to one or more solid supports e.g. a single support for microarray or fibre-optic assays, or multiple supports such as beads. The detection means is preferably a label (radioactive or dye, e.g. fluorescent) for labelling the expression products of the sample under test. The kit may also comprise means for detecting and analysing the binding profile of the expression products under test.

Alternatively, the binding members may be nucleotide primers capable of binding to the expression products, such that they can be amplified in a PCR. The primers may further comprise detection means, i.e. labels that can be used to identify the amplified sequences and their abundance relative to other amplified sequences.

The kit may also comprise one or more standard expression profiles retrievably held on a data carrier for comparison with expression profiles of a test sample. The one or more standard expression profiles may be produced according to the first aspect of the present invention.

The breast tissue sample may be obtained as excisional breast biopsies or fine-needle aspirates.

Again, the expression products are preferably mRNA or cDNA produced from said mRNA or cRNA. The binding members are preferably oligonucleotides fixed to one or more solid supports in the form of a microarray or beads (see above). The binding profile is preferably analysed by a detector capable of detecting the label used to label the expression products. The determination of the presence or risk of breast cancer can be made by comparing the binding profile of the sample with that of a control e.g. standard expression profiles.

In all of the aspects described above, it is preferred to use binding members capable of specifically binding (and, in the case of nucleic acid primers, amplifying) expression products of a said multigene classifier. This is because the expression levels of all genes make up the expression profile specific for the sample under test. The classification of the expression profile is more reliable the greater number of gene expression levels tested. Thus, preferably expression levels of more than 5 genes selected from one or more of said multi-gene classifiers are assessed, more preferably, more than 10, more than 20, more than 30, even more preferably, more than 40 and preferably all genes from a said multi-gene classifier. For example, the binding members may be capable of binding to expression products from all of the genes of Table S4, or a plurality of genes therefrom, as previously defined.

The known microarray and genechip technologies allow large numbers of binding members to be utilized. Therefore, the more preferred method would be to use binding members representing all of the genes in a said multigene classifier, or a plurality of genes therefrom, as previously defined for each multigene classifier. However, the skilled person will appreciate that a proportion of these genes may be omitted and the method still carried out in a reliable and statistically accurate fashion. In most cases, it would be preferable to use binding members representing at least 70%, 80% or 90% of the genes in a said multigene classifier. In this context, a multigene classifier preferably means the genes of Table S4 or a subset or group of a said Table. The multigene classifier may be the genes of Table A4.

Therefore, plurality may mean at least 50%, more preferably at least 70% and even more preferably at least 90% of the multigene classifier as mentioned above.

The provision of the genetic identifier allows diagnostic tools, e.g. nucleic acid microarrays to be custom made and used to predict, diagnose or subtype tumours. Further, such diagnostic tools may be used in conjunction with a computer which is programmed to determine the expression profile obtained using the diagnostic tool (e.g. microarray) and compare it to a “standard” expression profile characteristic of high confidence tumour v low confidence tumour. In doing so, the computer not only provides the user with information which may be used classifying the type of a tumour in a patient, but at the same time, the computer obtains a further expression profile by which to determine the “standard” expression profile and so can update its own database.

Thus, the invention allows, for the first time, specialized chips (microarrays) to be made containing probes corresponding to the said multigene classifiers, or a plurality of genes therefrom. The exact physical structure of the array may vary and range from oligonucleotide probes attached to a 2-dimensional solid substrate to free-floating probes which have been individually “tagged” with a unique label, e.g. “bar code”.

A database corresponding to the various biological classifications (e.g. high confidence or low confidence ER+/ER−) may be created which will consist of the expression profiles of various breast tissues as determined by the specialized microarrays. The database may then be processed and analysed such that it will eventually contain (i) the numerical data corresponding to each expression profile in the database, (ii) a “standard” profile which functions as the canonical profile for that particular classification; and (iii) data representing the observed statistical variation of the individual profiles to the “standard” profile.

In one embodiment, to evaluate a patient's sample, the expression products of that patient's breast sample (obtained via excisional biopsy or find needle aspirate) will first be isolated, and the expression profile of that sample determined using the specialized microarray. To classify the patient's sample, the expression profile of the patient's sample will be queried against the database described above. Querying can be done in a direct or indirect manner. The “direct” manner is where the patient's expression profile is directly compared to other individual expression profiles in the database to determined which profile (and hence which classification) delivers the best match. Alternatively, the querying may be done more “indirectly”, for example, the patient expression profile could be compared against simply the “standard” profile in the database. The advantage of the indirect approach is that the “standard” profiles, because they represent the aggregate of many individual profiles, will be much less data intensive and may be stored on a relatively inexpensive computer system which may then form part of the kit (i.e. in association with the microarrays) in accordance with the present invention. In the direct approach, it is likely that the data carrier will be of a much larger scale (e.g. a computer server), as many individual profiles will have to be stored.

By comparing the patient expression profile to the standard profile (indirect approach) and the pre-determined statistical variation in the population, it will also be possible to deliver a “confidence value” as to how closely the patient expression profile matches the “standard” canonical profile for high or low confidence tumours. This value will provide the clinician with valuable information on the trustworthiness of the classification, and, for example, whether or not the analysis should be repeated.

As mentioned above, it is also possible to store the patient expression profiles on the database, and these may be used at any time to update the database.

Aspects and embodiments of the present invention will now be illustrated, by way of example, with reference to the accompanying figures. Further aspects and embodiments will be apparent to those skilled in the art. All documents mentioned in this text are incorporated herein by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Identification of Tumours with Low Prediction Strength (“Low-confidence”).

Each sample in the training (a) and test set (b) is plotted (x-axis) against the sample's prediction strength (PS, y-axis). The training data set consists of 55 tumours and the test data set consists of 41 tumours. Samples exhibiting high positive PS values are classified as ER+, while samples with a high negative PS are ER−. Blue samples were correctly classified while red samples were misclassified. In general, a group of ‘low-confidence’ samples is observed (grey box) in both the training and test tumours.

FIG. 2. Kaplan-Meier analysis comparing the clinical behaviour of ‘high’ and ‘low-confidence’ tumours. Overall survival data in (a) and (b) is obtained from Stanford data set (9), while Time to Distance Metastasis data in (c) and (d) is obtained from Rosetta data set (10). Patients with ‘high-confidence’ tumours are depicted as green, while patients with ‘low-confidence’ tumours are depicted in pink. a) Overall survival of patients with ‘high’ (60 patients) and ‘low-confidence’ (14 patients) tumours regardless of ER status, b) Overall survival of patients with ER+‘high’ (48) and ‘low-confidence’ (7) tumours; c) Time from initial tumour diagnosis to appearance of distant metastasis of patients with ‘high’ (82) and ‘low-confidence’ (15) tumours regardless of ER status, (d) Time from initial tumour diagnosis to appearance of distant metastasis of patients with ER+‘high’ (63) and ‘low-confidence’ (5) tumours.

FIG. 3. widespread perturbations in ER-correlated genes in low Vs high confidence samples.

(a) and (b) Depicted are the relative expression levels of the top 122 ER discriminating genes (obtained from the SAM-133 gene set, see text) that are positively correlated to ER+ status in (a) ER+/High (yellow) and ER+/Low (turquoise), and (b) ER−/High (dark blue) and ER−/Low (pink) samples.

The order of the 122 genes along the x axis is determined by their S2N ratio (see Materials and Methods). The S2N metric for a particular gene takes into account both the difference in mean expression level between two classes, as well as the standard deviation in expression for that gene within each class being compared. Note that the specific order of the 122 genes in (a) and (b) are different, depending on their S2N ratio (Table 2). (c) and (d) depicted are the relative expression levels of the top 54 ER discriminating genes that are negatively correlated to ER+ status (11 belonging to the SAM-133 gene set, see supplementary info for details) in (c) ER/High (yellow) and ER+/Low (turquoise), and (d) ER−/High (dark blue) and ER−/Low (pink) samples. There are considerably less perturbations observed than in (a) and (b).

FIG. 4. ERBB2+ is associated with ‘low-confidence’ prediction across multiple breast cancer expression datasets. Data is taken from ref. 3. a) Identification of tumour samples (columns) expressing high levels of ERBB2 and other genes (MLN64, GRB7) physically linked to the 17 q ERBB2 chromosomal locus (rows). High expression is represented by a red square. Tumour samples 5141, 8443, 7636, 4527, 5955, 10444, 5985, 6936 exhibit high expression of ERBB2 and ERBB2-linked genes, while 6080 and 10188 exhibit elevated but weaker expression. b) Summary of ANN models for ER classification (adapted from FIG. 1 b in ref. 3). Tumour samples classified as ER+ are blue while ER− tumours are orange. Prediction confidence is represented by each sample's standard deviation (SD), with ‘low confidence’ samples having a high SD. The eight ‘highly expressing’ ERBB2+ve samples are depicted (ERBB2 at the left or right of the sample SD). Note that tumour samples with high SDs tend to be ERBB2+ve.

FIG. 5. Principle component analysis (PCA), a mathematical technique that provides a projection of complex data sets onto a reduced, easily visualized space, provides a useful visual assessment of how clearly the samples are discriminated on the basis of the SAM-133 gene set. ER+ and ER− tumours are clearly distinguishable from one another, while ERBB2+ samples lie in the intermediate space. Color-coding scheme: ER+ERBB2−, yellow; ER+ERBB2−, turquoise; ER−ERBB2+, blue; and ER−ERBB2+, pink. Color-coding scheme: ER+ ERBB2−, yellow; ER+ERBB2+, turquoise; ER− ERBB2−, blue; and ER− ERBB2+, pink. X-axis is principle component 1 and Y-axis is component 2. Samples that lie at the left of the red line are ER+ except two ER− samples; while the samples on the right are ER− samples except one misclassification. Samples close to the boundary (in the square) are all ERBB2+.

FIG. 6 shows the clinical prognoses of patients with ‘high-confidence’ ER negative tumours to those patients harboring ‘low-confidence’ ER negative tumours. Two independent data sets were analyzed, referred to as the ‘Rosetta’ and ‘Stanford’ data sets. FIG. 6( a) shows Rosetta tumours: Relapse free survival was measured. 11/19 (58%) High-confidence patients developed distant metastasis within 5 years; while in Low-confidence ER− the number is 8/10. (80%). FIG. 6( b) shows Stanford tumours: Overall survival was measured. 7/12 (58%) High-confidence patients are dead; while in Low-confidence ER− the number is 5/7 (71%).

FIG. 7 shows identification of Tumors with Low Prediction Strength (“Low-confidence”) in the Stanford and Rosetta Data Sets

RESULTS Classification of Breast Tumours by ER Status Using Expression Profiles from Chinese Patients Reveals a Distinct Population of ‘Low Confidence’ Samples

The overall incidence patterns of breast cancer in Caucasian and Asian populations are distinct (8), prompting the inventors to investigate if findings from previous reports (3, 4) could also be observed in their local patient population. They first used gene expression profile data to classify a set of breast tumours by their ER status. A training set of 55 breast tumours was selected, where the ER status of each tumour was pre-determined using IHC. Two classification methods were tested: weighted-voting (WV) and support vector machines (SVM), and classification accuracy was assessed through leave-one-out cross validation (LOOCV) (Supplementary Information). In addition to classifying a sample, quantitative metrics were used to provide an assessment of classification uncertainty (Materials and Methods). The overall classification accuracy on the training set was 95% (WV) and 96% (SVM), with seven samples characterized by ‘low confidence’ or marginal predictions (grey box, FIG. 1 a). To determine if such ‘low-confidence’ samples could also be observed in an independent set of tumours, a second set of 41 tumours was used as an independent test set. Although the overall classification accuracy on the independent test set was 91% (WV and SVM), nine samples once again displayed a ‘low-confidence’ prediction (FIG. 1 b). Thus, using two different classification methods (WV and SVM), certain breast tumours were found to exhibit a distinct ‘low-confidence’ character when being classified by ER status on the basis of their gene expression profiles.

Patients with ‘Low-Confidence’ Tumours Exhibit Decreased Overall Survival and Shorter Time to Distant Metastasis in Comparison to Patients with ‘High confidence’ Tumours

Since the differentiation of tumours into ‘high’ and ‘low-confidence’ sub-populations was achieved through a purely computational analysis of tumour gene expression profiles, it is unclear if this distinction is biologically or clinically meaningful, and if the use of gene expression profiles in this manner affords any substantial advantage over conventional immunohistochemical techniques to determine the ER status of breast tumours. To address this issue, the inventors investigated if the ‘low-confidence’ tumours might exhibit any clinical behaviors distinct from their ‘high-confidence’ counterparts. They used two publicly available breast cancer expression data sets for which related but distinct types of clinical information was available. The first set (9) consists of a cDNA microarray data set of 78 breast carcinomas and 7 nonmalignant samples with overall patient survival information (referred to as the Stanford data set). The second one (10) consists of 71 ER+ and 46 ER lymph-node negative tumours profiled using oligonucleotide-based microarrays, out of them 97 samples had the clinical information being the time interval from initial tumour diagnosis to the appearance of a new distant metastasis (referred to as the Rosetta dataset). The inventors used WV to classify the breast tumours in the Stanford and Rosetta datasets by their ER subtype. Consistent with their own data set, among the 56 ER+ and 18 ER tumours in the Stanford data set (4 tumours were removed due to lack of ER status information), they observed an overall LOOCV accuracy of 93%, with 14 tumours being classified as ‘low-confidence’. Similarly, the WV analysis also identified 15 tumours in the Rosetta data set as exhibiting a ‘low-confidence’ classification, with an overall LOOCV accuracy of 92%. These numbers are comparable to that observed in the inventors' own patient population.

They then compared the clinical behaviour of the ‘high’ and ‘low-confidence’ tumour populations using Kaplan-Meier analysis. As shown in FIG. 2, patients with ‘low-confidence’ tumours exhibited a significantly worse overall survival (p=0.0003, log rank test) and shorter time to distant metastasis (p=0.0001, log-rank test) than their ‘high confidence’ counterparts. This result indicates that the ‘high’ vs ‘low-confidence’ binary distinction is indeed clinically meaningful. The inventors then repeated this analysis, but first subdividing the tumours into independent ER+ and ER− categories. For ER+ tumours, they once again found that ‘low-confidence’ ER+ tumours were associated with a significantly worse overall survival (p=0.03, log-rank test) and shorter time to metastasis (p=0.004, log-rank test) (FIG. 2) than ‘high-confidence’ ER+ tumours. No statistically significant differences in overall survival and time to metastasis were observed for the ER− tumours. These results indicate that ER+ tumours can be subdivided on the basis of the ‘high’ and ‘low-confidence’ binary classification into distinct disease groups exhibiting different clinical behaviours. Since distinguishing between these two groups is currently not possible by conventional immunohistochemical methods used for ER detection, this result also demonstrates how gene expression profile data can be a useful adjunct to conventional strategies for breast cancer prognostication and staging.

‘Low-Confidence’ Tumours Exhibit Widespread Perturbations in the Expression of Genes Important for ER Subtype Discrimination

The classification algorithms used in these and other studies (e.g. WV, SVM, ANN, see below) all rely upon the combinatorial input of multiple discriminator genes whose individual contributions are then combined to arrive at a particular classification decision (i.e. if the tumour is ER+ or ER−). It is formally possible that the ‘low-confidence’ prediction status of these breast tumours is due to either the dramatic deregulation of a few key discriminator elements (i.e. specific effects), or the more subtle perturbation of a large number of discriminator genes (i.e. widespread effects). To distinguish between these two possibilities, the inventors compared the expression levels of genes important for ER subtype discrimination between ‘high’ and ‘low’ confidence tumours. First, to identify ER discriminating genes which where differentially regulated between ER+ and ER− tumours, they utilized a statistical technique called significance analysis of microarrays (SAM) (11).

Employing their combined dataset (total number=96 tumours), a total of 133 differentially regulated genes (SAM-133) were identified at a ‘false discovery rate’ (FDR) of 0% (the FDR is an index used by SAM to estimate the number of false positives—an FDR of 10% for 100 genes indicates that 10 genes are likely to be false positives). In this set, 122 genes were up-regulated in ER+ samples (ie positively correlated to ER status), while the remaining 11 were down-regulated in ER+ tumours (ie negatively correlated to ER). As predicted, the SAM-133 gene set includes a number of genes related to the ER pathway, such as ESR1, LIV1 (an estrogen-inducible genes), and TFF1, and some genes (e.g. GATA-3) were identified multiple times. A number of genes in the SAM-133 list are also found in similar lists reported by others (3, 4).

The inventors then subdivided the ER+ and ER− tumours each into ‘high’ and ‘low’ confidence categories (ie ER+/High, ER+/Low, ER−/High, ER−/Low), and the expression levels of the SAM-133 genes were compared between the groups (FIG. 3). Of the 122 genes in the SAM-133 gene set that were positively correlated to ER status, approximately 62% exhibited a significantly lower average expression level (referred as ‘perturbed expression’) in the ER+/Low samples compared to the ER+/High tumours (p<0.05, FIG. 3 a and Table 2). Genes with ‘perturbed’ expression included ER, GATA3, BCL2, IGF1R, and RARA, while other ER-discriminator genes, such as TFF1, TFF3 and XBP1 were unaffected. Similarly, in the ER− ‘high’ and ‘low’ confidence samples, the inventors witnessed a reciprocal pattern where approximately 42% of the 122 genes exhibited a higher average expression level in the ER−/Low samples compared to the ER−/High tumours (p<0.05, FIG. 3 b and Table 2). Intriguingly, although the expression levels of certain genes (e.g. GATA3, BCL2) were perturbed between ‘low’ and ‘high’ confidence samples in both the ER+ and ER− subtypes, the perturbation of other genes appeared to be subtype-specific. For example, ESR1 and IGFR1 were only perturbed in the ER+ samples, while XBP1 was only perturbed in the ER− samples. Finally, there were minimal changes in the expression levels of ER-discriminating genes that were negatively correlated to ER+ status (i.e. highly expressed in ER− tumours) (FIGS. 3 c and d). This result suggests that the expression perturbations observed in the ‘low-confidence’ samples, although widespread, are primarily observed in genes whose expression is positively correlated to ER (Supplementary Information).

Elevated Expression of the ERBB2 Oncogene is Significantly Associated with the ‘Low-Confidence’ Predictions

The expression perturbations observed in the ‘low-confidence’ breast tumours could be due to multiple reasons, ranging from experimental variation (e.g. poor sample quality, tumour excision and handling), choice of the classification method, to population and sample heterogeneity. To gain insights into the possible mechanisms underlying these expression perturbations, the inventors attempted to determine if there were any specific histopathological parameters that might be correlated to the ‘low-confidence’ state. No significant associations were observed between the ‘low-confidence’ status of a tumour and patient age, lymph node status, tumour grade, p53 mutation status or progesterone receptor status (Table 1). The inventors discovered, however, a significant positive association (p<0.001, Supplementary Information) between a tumours' ERBB2 status and a ‘low confidence’ prediction. This correlation, observed using the training set data, was then assessed using the independent test set samples. Of the nine ‘low-confidence’ samples in the independent test set, eight tumours were also ERBB2+(8/9), indicating that this association is not dataset-specific.

The inventors also investigated if the correlation between the ‘low-confidence’ predictions with high ERBB2 expression could have been independently discovered by comparing the global expression profiles of ‘high’ and ‘low’ confidence tumours. First, they compared the ‘high-confidence’ and ‘low-confidence’ tumours belonging to the ER+ subtype. A total of 89 genes were identified as being significantly regulated (FDR=14%). Among the top 50 most significantly up-regulated genes in the ER+‘low-confidence’ samples, 3 genes—PMNT (ranked 4th), GRB7V (8th), and ERBB2 (36th) were of particular interest (Supplementary Information), as they are all physically located on the 17 q region, a frequent target of DNA amplification in breast cancer (12). In a separate analysis, the ER− ‘high-confidence’ and ER− ‘low-confidence’ samples were also compared. Among the top 50 genes identified as being differentially regulated (FDR=4%), the inventors once again identified the 17 q genes PMNT (ranked 5th), GRB7V (10th) and ERBB2 (28th) as exhibiting increased expression in the ‘low-confidence’ samples (Supplementary Information). Taken collectively, these results suggest that for both the ER+ and ER− subtypes, the ‘low-confidence’ breast tumours are significantly associated with increased expression of ERBB2 in comparison to the ‘high confidence’ tumours, most likely resulting from DNA amplification of the 17 q locus. However, please note that the association between ‘low-confidence’ prediction and ERBB2+ expression, although highly significant, is not perfect, as a few tumours that were designated as ERBB2+ by conventional IHC exhibited ‘high-confidence’ predictions, while not all ‘low-confidence’ tumours are ERBB2+. One possibility may be that other genes, besides ERBB2, may also contribute to a breast tumour exhibiting a ‘low-confidence’ state.

To validate their finding, the inventors then analyzed the other independently derived breast cancer expression datasets. First, of the nine ERBB2+ tumours in the Stanford data set, all nine were predicted as being in the ‘low-confidence’ group (p<0.001, Supplementary Information). Second, in the Rosetta data set, they once again found a significant association between the confidence level of prediction and ERBB2 expression (p<0.001, Supplementary Information). Third, Gruvberger and his colleagues utilized artificial neural networks (ANNs) on a cDNA microarray data set of 28 ER+ and 30 ER− samples to predict the ER status of breast tumours (3). Their results, shown in FIG. 4 b, depicts the output of the ANN model with sample standard deviations (SDs), as assessed using the top 100 discriminator genes for ER subtype. Samples with a wide SD are analogous to the ‘low-confidence’ status of the WV and SVM methodologies. As can be seen from FIG. 4 b, ERBB2+ samples (determined in FIG. 4 a) tend to be associated with large SDs, which indicate high uncertainty, particularly for ER+ tumours. Taken collectively, the association between the confidence level of ER prediction and ERBB2 status was observed on a wide range of data sets originating from different laboratories utilizing different microarray technologies (Affymetrix, cDNA and oligonucleotide) on different patient populations (Asian, European/Caucasian), and predicted by different classification algorithms (WV, SVM, ANN). The commonality of these results on both the inventor data set and publicly available data sets suggests that the correlation between high ERBB2 expression to ‘low-confidence’ prediction status may be an inherent feature of breast cancer in general.

A Significant Proportion of Genes Perturbed in the Low Confidence Samples are not Known to be Regulated by Estrogen and Lack Potential EREs in their Promoters

The strong correlation between high ERBB2 levels and the widespread perturbations of ER-subtype discriminating genes observed in the ‘low-confidence’ tumours raises the possibility that ERBB2 may be functionally contribute towards this phenomenon. One possible mechanism by which this could occur is through ERBB2 signaling which has been proposed to inhibit the transcriptional activity of ER (see Discussion). Under this scenario, one might expect that a significant proportion of the genes perturbed between the ‘high-confidence’ (ERBB2−) and ‘low-confidence (ERBB2+) tumours would consist of genes regulated by ER. The inventors tested this hypothesis in two ways. First, they compared their list of significantly-perturbed genes (Table 2) to SAGE expression data derived from estrogen (E2) stimulated MCF-7 cells (13) to determine if the extent of overlap between the two. Only two genes (STC2, TFF1) were found in common between the SAGE data and the ‘perturbed’ gene list, and one (TFF1) was regulated in the opposite manner from that expected, exhibiting higher expression in the ERBB2+ samples. This result, within the limits of the cell line assay, suggests that many of the ‘perturbed’ genes in the ‘low confidence’ tumours may not be directly regulated by estrogen. Second, as in-vitro cell line studies may not fully recapitulate the effects of estrogen in vivo, the inventors then adopted a bioinformatics approach using a recently described algorithm, Dragon Estrogen Response Element Finder (DEREF), to search for putative estrogen-response elements (EREs) in the promoter regions of the perturbed genes (14). The prediction accuracy of DEREF has been validated in a number of in vivo examples—it detects ERE patterns 2.8× more frequently in the promoter regions of estrogen responsive versus non-responsive genes in a microarray experiment, and 5.4× more frequently in the promoters of genes belonging to the estrogen-induced SAGE dataset versus genes whose expression is negatively correlated to ER in breast cancers (Supplementary Information). Of the top 50 perturbed genes in the ER+tumours (Table 2), the transcriptional start sites of 35 could be accurately determined and thus were subsequently analyzed by DEREF. Of this 35, EREs were detected with high-confidence in only 12 promoters (total frequency 34%) (Table 2).

Conversely, of the top 50 perturbed genes in the ER− tumours, 33 were analyzed by DEREF and high-confidence EREs were detected in only 3 (total frequency 9%) (Table 2). Thus, EREs were detected in the promoters of perturbed genes in ER+ tumours at 3.7× higher frequency than in the ER− tumours. This difference was significant by a chi-square analysis (p=0.012), suggesting that ERBB2 may affect transcription in ER+ and ER tumours via distinct mechanisms (see Discussion). Regardless, EREs were not detected as over represented in the perturbed genes in both subtypes (ER+ and ER−), suggesting that these genes may not be direct transcriptional targets of ER. These genes may represent either indirect targets of ER, or may be transcriptionally regulated via ER-independent mechanisms.

Definition of a Optimal Gene Set to Classify Low and High Confidence Tumours Irrespective of ER Subtype

The objective of this analysis was to identify an optimal set of genes which could be used to classify “high” and “low-confidence” tumours regardless of their ER status.

Details

A total of 96 tumours were analyzed, of which 16 were LC and 80 were HC. A series of three independent analytical methods (SAM, GR, and WT, see below) were used to identify genes that were differently regulated between the two groups (LC and HC). The ability of these gene sets to classify the HC or LC status of a tumour was assessed by a leave-one-out cross validation assay using either Support Vector Machine or Weighted Voting as the classification algorithm.

Results

SAM (Significance Analysis of Microarrays): At a FDR (False-discovery rate) of <15%, a total of 86 up-regulated and 2 down-regulated genes in low-confidence tumours were identified. Using this gene set, the LOOCV assay produced a classification accuracy of 84%. The 88 genes are shown in Table A1.

GR (Gene Ranking by SVM): A total of 251 genes were identified with the ability to classify the HC or LC status of a tumour, with a classification accuracy of 86%. The 251 genes are shown in Table A2.

WT (Wilcoxon Test): At a P-value of <0.05 and a >=2-fold change cutoff, a total of 38 genes were identified. This 38 gene set delivered a LOOCV accuracy of 80%. The 38 genes are shown in Table A3.

13 ‘common’ genes among the three gene sets (SAM-88, GR-251, WT-38) were then identified. This 13 member gene achieved a classification accuracy of 84% by LOOCV. In essence, these 13 ‘common genes’ are robust significant markers and can archive comparable performance as other ‘complete’ marker sets. Hence they could be taken as ‘optimal’ genes. The 13 genes are shown in Table A4.

Clinical Outcome of ER Negative ‘High-Confidence’ vs ‘Low-Confidence’ Tumours

The objective of this analysis was to compare the clinical prognoses of patients with ‘high-confidence’ ER negative tumours to those patients harbouring ‘low-confidence’ ER negative tumours.

Details

Two independent data sets were analysed, referred to as the ‘Rosetta’ and ‘Stanford’ data sets. The Rosetta data set contains 29 ER negative tumours, of which 19 are ‘high-confidence’ while 10 are ‘low-confidence’. The Stanford data set contains 19 ER negative tumours, of which 12 are ‘high-confidence’ and 7 are ‘low-confidence’. The results of the analysis are shown in FIGS. 6( a) and 6(b).

In both cases, patients with ‘low-confidence’ tumours exhibited a worse prognosis than their high-confidence counterparts. Although this difference is not statistically significant, this may be due to low numbers of patients analyzed in these studies.

Discussion

The findings in this report complement and extend the previous work in this area related to the classification of breast tumours by ER subtype. In general, these studies have shown that while gene expression data can be successfully used to classify the ER subtype of most tumours, there invariably exists a certain population of tumours that exhibit a low-confidence of prediction and thus cannot be accurately classified (3, 4). The inventors decided to investigate these ‘low-confidence’ samples, by performing an in-depth analysis of these ‘low-confidence’ tumours. They made a number of surprising findings. They found that in comparison to patients with ‘high-confidence’ tumours, patients with ‘low-confidence’ tumours exhibited a significantly worse overall survival and shorter time to distant metastasis. The ‘high’ vs ‘low-confidence’ classification, arrived at by computational analysis of gene expression profiles, also served to separate ER+ tumours into groups exhibiting distinct clinical behaviours (FIG. 2). As the discernment of such subgroups is currently not possible using conventional immuno-histopathological techniques, these results also demonstrate how the classification of a breast tumour's ER status by expression profiling and computational analysis can be medically extremely useful.

The inventors also made the surprising finding that the ‘low-confidence’ state is significantly associated with elevated expression of the ERBB2 receptor. However, they emphasize that the connection between ERBB2 and ‘low-confidence’ predictions remains an association, and that at this point they have no evidence (from their own data) that ERBB2 is functionally responsible for causing the ‘low-confidence’ state. Nevertheless, given that ER and ERBB2 are currently the two most clinically relevant molecular biomarkers in breast cancer, it is tempting to speculate that these results suggest that there may exist substantial cross-talk between these two signaling pathways in breast cancer, a possibility that has also been proposed by others (7). Intriguingly, the association between ERBB2+ and ‘low-confidence’ prediction, although highly significant, is not perfect, as a few ERBB2+ tumours were also found to exhibit ‘high-confidence’ predictions, while not all ‘low-confidence’ tumours are ERBB2+. Thus, it is unlikely the ‘low-confidence’ population of breast tumours could have been discerned by conventional histopathological techniques used to detect ERBB2 such as IHC and FISH. Instead, the inventors believe that for tumours designed ERBB2+ by routine histopathology, that the further examination of these tumours for the presence of such characteristic ‘expression perturbations’ may be a promising method to distinguish between tumours that are likely to be more clinically aggressive versus those that will progress along a comparatively more indolent course.

Exploring this possibility will be an important task for future research. Clinically, elevated ERBB2 expression in ER+ breast tumours has long been associated with decreased sensitivity to anti-hormonal therapies, and a number of experimental papers have been reported addressing possible mechanisms by which ERBB2 activity might cause this effect. In general, the most popular model has been one in which elevated ERBB2 signaling causes ER to exhibit diminished transcriptional activity, either through transcriptional down-regulation of the ER gene (17), posttranslational modifications of ER (e.g. phosphorylation) (18), or via induction of ER binding corepressors such as MTA1 (19). If the effects of ERBB2 were mediated primarily through effects on ER transcriptional activity, then one might expect that a substantial number of the genes whose transcription is significantly perturbed in the ERBB2+‘low-confidence’ samples should correspond to genes which are direct targets of ER. The inventors found, however, that a significant proportion of the genes that were significantly perturbed in both ER+ and ER− tumours have not been previously identified as estrogen-induced genes, and these genes also appear to lack potential EREs in their promoters. This is particularly the case in the ER− tumours, in which only 9% of the significantly perturbed genes were found to contain high-confidence putative EREs in their promoters. Although the inventors cannot rule out the possibility that these perturbed genes may be indirect targets of ER or may be activated by ER via non-ERE mechanisms, these findings raise the possibility that ERBB2 activity may regulate a significant fraction of genes in breast tumours in an ER-independent fashion. There are numerous avenues by which this could occur. For example, ERBB2 might regulate other transcription factors besides ER through activation of the RAS/MAPK or PI3/Akt pathways (18).

Alternatively, ERBB2 activity may results in the induction of chromatin factors such as MTA1 which may play more pleiotropic effects (19).

Materials and Methods

Breast Tissue Samples and Patient Data Breast tissue samples and clinical data were obtained from the Tissue Repository in the institution National Cancer Center of Singapore, after appropriate approvals had been obtained from the institution's Repository and Ethics Committees. Samples were grossly dissected in the operating theater immediately after surgical excision, and flash-frozen in liquid N2. Histological information (ER, ERBB2) was provided by the Department of Pathology at Singapore General Hospital, and samples were selected to provide a comparable number of ER+ and ER− tumours (as determined by IHC) for each data set.

Tumour samples contained >50% tumour content as assessed by cryosections. 55 tumours (35 ER+ samples and 20 ER− samples), was used as training data, while a separate set of 41 tumours (21 ER+ and 20 ER− samples) was used for blind testing. A detailed list of all samples and clinical data for the patient is included in Table S1.

Sample Preparation and Microarray Hybridization

RNA was extracted from tissues using Trizol reagent and processed for Affymetrix Genechip hybridizations using U133A Genechips according to the manufacturer's instructions.

Data Preprocessing

Raw chip scans were quality controlled using the Genedata Refiner program and deposited into a central data storage facility. The expression data was pre-processed by removing genes whose expression was absent throughout all samples (i.e. ‘A’ calls), subjecting the remaining genes to a log 2 transformation, and mediate-centering by samples.

Prediction of ER Status

Two classification algorithms, weighted voting (WV) (20) and support vector machines (SVMs) (21), were used to classify breast tumours according to ER subtype. Classification accuracy is defined as the number of correctly classified samples divided by the total number of samples. For the WV analyses, classification accuracy was determined using a gene set of the top 50 discriminating genes for ER status, while the SVM-based binary classifier utilized all genes.

Weighted Voting (WV): The weighted voting algorithm utilizes a signal-to-noise (S2N) metric to perform binary classifications. Each gene belonging to a predictor set is assigned a ‘vote’, expressed as the weighted difference between the gene expression level in the sample to be classified and the average class mean expression level. Weighting is determined using the correlation metric

${P\left( {g,c} \right)} = \frac{\mu_{1} - \mu_{2}}{\sigma_{1} + \sigma_{2}}$

(μ and σ denotes means and standard deviations of expression levels of the gene in each of the two classes). The ultimate vote for a particular class assignment is computed by summing all weighted votes made by each gene used in the class discrimination. The “prediction strength” (PS) is defined as:

${PS} = \frac{V_{WIN} - V_{LOSE}}{V_{WIN} + V_{LOSE}}$

where V_(WIN) and V_(LOSE) are the vote totals for the winning and losing classes, respectively. PS reflects the relative margin of victory and hence provides a quantitative reflection of prediction certainty.

Support Vector Machine (SVM): Support Vector Machines are classification algorithms which define a discrimination surface in the utilized feature (gene) space that attempts to maximally separate classes of training data (21). An unknown test sample's position relative to the discrimination surface determines its class. Distances are usually calculated in the n-dimensional gene space, corresponding to the total number of gene expression values considered. The inventors used SVM-FU (available at www.ai.mit.edu/projects/cbcl/) with the linear kernel to implement the SVM analysis. The confidence of each SVM prediction is based on the distance of a test sample from the discrimination surface, as previously described (22).

Identification of Low Confidence Tumours

Due to the clinical importance of achieving good prediction confidence, the inventors conservatively chose a high confidence threshold to minimize potential false positive classifications. On the basis of the leave-one-out cross validation (LOOCV) results, they used a threshold of 0.4 and identified 16 samples (out of a total of 96) as being in the ‘low confidence’ group. A tumour sample was assigned to the “low-confidence” category if its prediction strength (PS) from WV was less than this threshold.

Selection of Differentially Expressed Genes and Determination of Expression Perturbations Significance analysis of microarrays (SAM) is a statistical methodology developed to identify genes that are differentially expressed between separate groups (11). Genes are ranked are according to their statistical likelihood of being regulated. The SAM algorithm also performs a permutation analysis of the expression data to estimate the number of genes identified as being ‘differentially regulated’ by random chance (i.e. false positives). This number is the ‘false discovery rate’ (FDR). Depending upon the desired stringency, different reports have used FDRs ranging from <5% to 33% (23, 24).

Student's t-test was used to compare levels of expression in the SAM-133 gene set between ‘high’ and ‘low-confidence’ groups. A gene was classified as exhibiting significant ‘perturbed expression’ if its p-value was less than 0.05.

Computational Identification of Estrogen Response Elements (EREs) using DEREF A computational algorithm, Dragon ERE Finder (DEREF) (14), was used to identify putative estrogen response elements (EREs), which are DNA binding sites of ER within promoters (see http://sdmc.lit.org.sg/ERE-V2/index for a description of the underlying methodology of DEREF). On the default setting, DEREF produces on average one ERE pattern prediction per 13,000 nt on human genomic DNA, with a sensitivity of 83%. To reduce the number of false positives, the inventors applied in this report an additional criteria that a predicted ERE pattern of 17 nucleotides (14) also had to match (based on BLAST (25) matching without allowed gaps) a similar ERE pattern from at least one other human gene promoter, under conditions where the latter pattern could be predicted by DEREF at a sensitivity of 97%. The ERE searches in this report were performed against a database of approximately 11,000 reference human promoter sequences covering the range [−3000, +1000] relative to the 5′end of the gene, which was generated using the FIE2 program (26, 27). Some genes to be analyzed were not contained in this promoter database, and the ERE searches for these genes were thus not performed. Such genes are denoted in Table 2 by N/A.

Identification of Tumours with Low Prediction Strength (“Low-Confidence”) in Stanford and Rosetta Data Sets

Weighted Voting and Leave One Out Cross Validation was independently performed for two independent data sets (referred to as “Stanford” and “Rosetta” data sets). The results are plotted in a similar manner to those of FIG. 1, and the plots are shown in FIG. 7. In both data sets, the low-confidence tumours can be identified as the points at which tumours begin to demonstrate qualitatively reduced prediction strengths (PS's) (the ‘cliff-points’) from the majority of the tumour population. Although each dataset was analysed independently, the proportions of ‘low-confidence’ tumours for all datasets are highly comparable, ranging from 15-19% of all tumours (Rosetta data set shown in FIG. 7( a)=18/117 (15.4%); Stanford data set shown in FIG. 7( b)=14/74 (18.9%)), our data set=16/96 (16.7%))

Details of Different Array Technologies Used to Produce FIG. 7 Data

Stanford data set: This data was produced using 2-colour cDNA microarrays, in which PCR-amplified cDNA fragments (representing different genes) were robotically deposited onto a solid substrate to create the microarray

Rosetta data set: This data was produced using 2 colour oligonucleotide microarrays, in which 70-80mer oligonucleotides (representing different genes) were chemically synthesized in-situ on a solid substrate to create the microarray.

Details of Patient Populations

The Stanford data set consists of cDNA microarray data for 78 breast carcinomas (tumours) and 7 nonmalignant samples with overall patient survival information.

The Rosetta set consists of 117 early stage (lymph-node negative) breast tumours profiled using oligonucleotide-based microarrays

Population Size

As shown above, the low-confidence tumours occupy around 15-19% of each breast tumour population. To confidently identify this tumour subpopulation, a minimum data set of at least 25-30 profiles, preferably higher (around 80-100 tumours, as in the three data sets above) is preferably required.

Sample Data

Table S7 shows the mean (μ) and standard deviation (σ) parameters for use in a Weighted Voting algorithm for each gene of the SAM-133 geneset. These data could be used to assign the an unknown breast tumour sample as high or low confidence, given a set of expression levels for genes of the SAM-133 geneset. The genes of Table 2 are included in the SAM-133 geneset. The data is specific to Weighted Voting techniques applied to expression data from the Affymetrix U133 genechip.

Table S8 shows expression data for the Table A4 multigene classifier (common 13 genes) across high confidence and low confidence samples. The data are specific for the Affymetrix U133A genechip and have been through data preprocess. The gene expression profiles of the Table A4 multigene classifier can be used as training data to build a predictive model (eg, WV and SVM), which then can assign the confidence of an unknown breast tumour.

The data is tab delimited, and has the following format:

Columns:

1st column: Probe-ID of prognostic set genes 2nd column: Gene Name 3rd and other columns: gene expression data

Rows:

1st row: Sample Ids (35 samples) 2nd row: Confidence (high or low) of sample. 3rd and other rows: gene expression data

The gene expression data is derived as described in the ‘Sample Preparation and Microarray Hybridization’ and ‘Data Preprocessing’ (see Materials and Methods section).

Table S9 shows the mean (μ) and standard deviation (σ) parameters for use in a Weighted Voting algorithm for each gene of the Table A4 geneset. These data could be used to assign the an unknown breast tumour sample as high or low confidence, irrespective of ER status of the tumour, given a set of expression levels for genes of the Table A4 geneset.

The data is specific to Weighted Voting techniques applied to expression data from the Affymetrix U133 genechip.

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TABLE 1 Association Between Clinical Parameters and ER Classification Confidence Training Data Set (This Report) Stanford data set No. of Mean P No. of Mean P Patameter patients Confidence value Parameter patients Confidence value ERBB2 <0.001 ERBB2 <0.001 Positive 18 0.58 Positive 9 0.233 Negative 37 0.89 Negative 65 0.667 Age 0.45 Age 0.03 <55 yr 25 0.76 <55 yr 33 0.545 >=55 yr 30 0.81 >=55 yr 41 0.669 Node 0.98 Node 0.91 0 21 0.787 0 22 0.619 1-2 30 0.785 1-2 52 0.612 Histology 0.98 Histology 0.28 grade grade I 7 0.804 I 9 0.727 II 36 0.784 II 32 0.631 III-IV 8 0.779 III 32 0.583 PR 0.03 TP53 0.11 Positive 19 0.88 wild type 38 0.659 Negative 31 0.71 mutation 36 0.567

Table 2. The top 50 genes that are significantly perturbed between ER+/Low and ER+/High samples (a), and ER−/Low and ER−/High samples (b). In the ERE column, “ERE” indicates that the promoter contains a high confidence putative ERE as predicted by DEREF, “non-ERE” indicates that a putative ERE was not found, while “Low” indicates that an ERE was found for that promoter at medium confidence. N/A means that the promoter was not analyzed as it was not possible to determine their transcription start sites based on full-length transcripts. Genes are ranked in order of their S2N ratio between High and Low-confidence samples.

TABLE 2 Gene Name UniGene ERE Rank (a) ER+/Low vs. ER+/High estrogen receptor 1 Hs.1657 Non-ERE 1 dynein, axonemal, light intermediate polypeptide 1 Hs.406050 Low 2 cytochrome c oxidase subunit VIc Hs.351875 Non-ERE 3 annexin A9 Hs.279928 ERE 4 N-acetyltransferase 1 (arylamine N-acetyltransferase) Hs.155956 ERE 5 cytochrome P450, subfamily IIB (phenobarbital-inducible), Hs.1360 Low 6 polypeptide 6 retinoic acid receptor, alpha Hs.361071 ERE 7 insulin-like growth factor 1 receptor Hs.239176 N/A 8 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 Hs.76353 Low 9 antiproteinase, antitrypsin), member 5 Homo sapiens cDNA: FLJ21695 fis, clone COL09653, mRNA Hs.306803 N/A 10 sequence B-cell CLL/lymphoma 2 Hs.79241 ERE 11 GREB1 protein Hs.193914 Non-ERE 12 RNB6 Hs.241471 ERE 13 GATA binding protein 3 Hs.169946 Non-ERE 14 Homo sapiens mRNA; cDNA DKFZp564F053 (from clone Hs.71968 N/A 15 DKFZp564F053), mRNA sequence WW domain-containing protein 1 Hs.355977 Non-ERE 16 GDNF family receptor alpha 1 Hs.105445 Non-ERE 17 chromosome 1 open reading frame 34 Hs.125783 N/A 18 lymphoid nuclear protein related to AF4 Hs.38070 N/A 19 interleukin 6 signal transducer (gp130, oncostatin M receptor) Hs.82065 Non-ERE 20 regulator of G-protein signalling 11 Hs.65756 ERE 21 Human insulin-like growth factor 1 receptor mRNA, 3′ sequence, Hs.405998 N/A 22 mRNA sequence hepsin (transmembrane protease, serine 1) Hs.823 Non-ERE 23 sema domain, immunoglobulin domain (Ig), short basic domain, Hs.82222 Non-ERE 24 secreted, (semaphorin) 3B UDP-glucose ceramide glucosyltransferase Hs.432605 ERE 25 cytochrome P450, subfamily IIB (phenobarbital-inducible), Hs.330780 N/A 26 polypeptide 7 troponin T1, skeletal, slow Hs.73980 N/A 27 microtubule-associated protein tau Hs.101174 Non-ERE 28 seven in absentia homolog 2 (Drosophila) Hs.20191 Non-ERE 29 progesterone receptor Hs.2905 Non-ERE 30 KIAA0882 protein Hs.90419 N/A 31 hypothetical protein FLJ20151 Hs.279916 Low 32 ATP-binding cassette, sub-family A (ABC1), member 3 Hs.26630 ERE 33 carbonic anhydrase XII Hs.5338 ERE 34 solute carrier family 16 (monocarboxylic acid transporters), member 6 Hs.114924 Low 35 hypothetical protein FLJ12910 Hs.15929 Non-ERE 36 hypothetical protein FLJ20627 Hs.238270 Non-ERE 37 trichorhinophalangeal syndrome I Hs.26102 Non-ERE 38 calsyntenin 2 Hs.12079 N/A 39 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 Hs.234726 ERE 40 antiproteinase, antitrypsin), member 3 vav 3 oncogene Hs.267659 Non-ERE 41 LIV-1 protein, estrogen regulated Hs.79136 N/A 42 Homo sapiens mRNA; cDNA DKFZp434E082 (from clone Hs.432587 N/A 43 DKFZp434E082), mRNA sequence adenylate cyclase 9 Hs.20196 ERE 44 KIAA0876 protein Hs.301011 N/A 45 heme binding protein 1 Hs.294133 ERE 46 stanniocalcin 2 Hs.155223 Low 47 complement component 4B Hs.433721 N/A 48 solute carrier family 27 (fatty acid transporter), member 2 Hs.11729 N/A. 49 T-box 3 (ulnar mammary syndrome) Hs.267182 Non-ERE 50 (b) ER−/Low vs. ER−/High hypothetical protein FLJ20151 Hs.279916 Low 1 carbonic anhydrase XII Hs.5338 Low 2 GATA binding protein 3 Hs.169946 Non-ERE 3 homolog of yeast long chain polyunsaturated fatty acid elongation Hs.250175 Non-ERE 4 enzyme 2 WW domain-containing protein 1 Hs.355977 Non-ERE 5 X-box binding protein 1 Hs.149923 Non-ERE 6 adipose specific 2 Hs.74120 Low 7 melanoma antigen, family D, 2 Hs.4943 N/A 8 anterior gradient 2 homolog (Xenepus laevis) Hs.91011 Non-ERE 9 cytochrome c oxidase subunit VIc Hs.351875 Non-ERE 10 aldo-keto reductase family 7, member A3 (aflatoxin aldehyde Hs.284236 N/A 11 reductase) tight junction protein 3 (zona occludens 3) Hs.25527 N/A 12 LAG1 longevity assurance homolog 2 (S. cerevisiae) Hs.285976 ERE 13 inositol 1,4,5-triphosphate receptor, type 1 Hs.198443 Non-ERE 14 fructose-1,6-bisphosphatase 1 Hs.574 ERE 15 KIAA0882 protein Hs.90419 N/A 16 hypothetical protein FLJ12910 Hs.15929 Non-ERE 17 LIV-1 protein, estrogen regulated Hs.79136 N/A 18 methylcrotonoyl-Coenzyme A carboxylase 2 (beta) Hs.167531 Non-ERE 19 cytochrome P450, subfamily IIB (phenobarbital-inducible), Hs.330780 N/A 20 polypeptide 7 trefoil factor 3 (intestinal) Hs.82961 Low 21 Human clone 23948 mRNA sequence Hs.159264 N/A 22 N-acetyltransferase 1 (arylamine N-acetyltransferase) Hs.155956 Low 23 GREB1 protein Hs.193914 Non-ERE 24 retinoic acid induced 3 Hs.194691 Non-ERE 25 solute carrier family 16 (monocarboxylic acid transporters), member 6 Hs.114924 Low 26 dynein, axonemal, light intermediate polypeptide 1 Hs.406050 Low 27 solute carrier family 7 (cationic amino acid transporter, y+ system), Hs.22891 Low 28 member 8 WD repeat domain 10 Hs.70202 Non-ERE 29 calsyntenin 2 Hs.12079 N/A 30 v-myb myeloblastosis viral oncogene homolog (avian) Hs.1334 Low 31 trefoil factor 1 (breast cancer, estrogen-inducible sequence Hs.350470 Low 32 expressed in) hypothetical protein MGC2601 Hs.124915 ERE 33 dachshund homolog (Drosophila) Hs.63931 Non-ERE 34 mucin 1, transmembrane Hs.89603 N/A 35 complement component 4B Hs.433721 N/A 36 cysteine-rich protein 1 (intestinal) Hs.423190 N/A 37 NPD009 protein Hs.283675 Low 38 sema domain, immunoglobulin domain (Ig), short basic domain, Hs.82222 Non-ERE 39 secreted, (semaphorin) 3B HRAS-like suppressor 3 Hs.37189 N/A 40 ATP-binding cassette, sub-family A (ABC1), member 3 Hs.26630 Low 41 microtubule-associated protein tau Hs.101174 Non-ERE 42 Myosin VI [Homo sapiens], mRNA sequence Hs.385834 N/A 43 CGI-49 protein Hs.238126 N/A 44 retinoic acid receptor, alpha Hs.361071 Low 45 vav 3 oncogene Hs.267659 Non-ERE 46 chromosome 1 open reading frame 34 Hs.125783 N/A 47 estrogen receptor 1 Hs.1657 Non-ERE 48 solute carrier family 27 (fatty acid transporter), member 2 Hs.11729 N/A 49 TBX3-iso protein Hs.332150 N/A. 50

TABLE S1 Clinical information of breast tumor samples. Table S1. Clinical Information for our data sets Sample ID ER ERBB2* PR AGE NODE STAGE RACE The initial collection (55 samples) 980177 + neg + 75 2 IIIA CHINESE 980178 + neg − 69 1 IIB CHINESE 980194 − pos − 58 1 IIB CHINESE 980197 + pos + 55 1 IIB CHINESE 980203 + neg + 44 0 I CHINESE 980208 + neg + 42 1 IIB CHINESE 980214 + pos − 49 1 IIIB CHINESE 980215 + neg − 54 CHINESE 980216 − neg − 65 1 IIB Indian 980217 + neg 54 1 IIB CHINESE 980220 + pos 43 0 IIA CHINESE 980221 + neg + 34 1 IV CHINESE 980238 − pos 62 CHINESE 980247 − neg 35 CHINESE 980261 + neg − 60 CHINESE 980338 − neg − 55 0 IIA CHINESE 980346 + neg + 54 0 I CHINESE 980353 − neg − 59 0 IIA CHINESE 980373 − pos − 77 0 IIA CHINESE 980380 − pos − 55 0 I CHINESE 980383 + neg 66 0 IIA CHINESE 980391 + neg + 56 0 I CHINESE 980395 − pos − 68 1 IIB CHINESE 980396 − pos − 66 1 IIB CHINESE 980403 + neg + 73 0 IIA CHINESE 980404 + neg + 46 1 IIB CHINESE 980409 + neg − 48 0 I CHINESE 980411 − neg − 72 0 IIA CHINESE 980434 + neg + 73 0 IIA CHINESE 980441 − neg − 66 1 IIB CHINESE 990075 + neg + 66 1 IIB CHINESE 990082 + neg + 49 1 IIB CHINESE 990107 + neg − 51 1 IIB Indian 990113 + neg + 70 1 IIIA CHINESE 990115 + pos + 38 1 IIB CHINESE 990123 + neg + 53 1 IIIA CHINESE 990134 − pos − 43 0 IIA CHINESE 990148 + pos − 60 1 IIB CHINESE 990174 − neg − 56 1 IIB CHINESE 990223 + pos − 52 1 IIA CHINESE 990262 − pos − 68 1 IIB CHINESE 990299 − neg − 58 1 IIIA CHINESE 990375 + neg − 38 0 I CHINESE 2000209 + pos − 58 0 IIA CHINESE 2000422 + neg + 52 1 IIIA CHINESE 2000500 − neg − 44 1 IV CHINESE 2000683 + neg + 72 0 IIA CHINESE 2000759 − pos − 57 0 I CHINESE 2000768 + neg + 39 0 IIA CHINESE 2000775 + neg − 51 0 IIA CHINESE 2000779 + neg − 48 0 IIB CHINESE 2000804 + neg + 39 1 IIB CHINESE 2000813 − pos − 60 1 IIB CHINESE 2000829 − pos − 51 1 IIB CHINESE 2000948 + neg − 56 1 IIB CHINESE The second collection (41 samples) 980058 + neg 72 CHINESE 980193 − neg 49 CHINESE 980256 − neg 46 CHINESE 980278 + neg 64 CHINESE 980285 − neg 49 CHINESE 980288 + pos 45 INDIAN 980315 − neg 59 CHINESE 980333 + neg 51 CHINESE 980335 − pos 33 CHINESE 2000104 + pos 59 CHINESE 2000171 − pos 50 CHINESE 2000210 − pos 50 MALAY 2000215 + neg 50 CHINESE 2000220 + neg 52 CHINESE 2000237 + pos 43 CHINESE 2000272 + neg 50 INDIAN 2000274 + neg 40 CHINESE 2000287 − pos 53 CHINESE 2000320 − neg 67 CHINESE 2000376 − pos 65 CHINESE 2000399 − P05 44 CHINESE 2000401 + neg 51 CHINESE 2000593 − neg 60 CHINESE 2000597 + neg 57 CHINESE 2000609 + neg 62 CHINESE 2000638 − neg 60 CHINESE 2000641 − pos 47 MALAY 2000651 + neg 45 CHINESE 2000652 − pos 56 CHINESE 2000675 − pos 78 CHINESE 2000709 − pos 45 CHINESE 2000731 − neg 68 INDIAN 2000787 + neg 57 CHINESE 2000818 + neg 52 CHINESE 2000880 − neg 54 CHINESE 20020021 + neg 64 CHINESE 20020051 + neg 38 MALAY 20020056 + neg 71 INDIAN 20020071 + neg 58 CHINESE 20020090 − pos 60 CHINESE 20020160 + neg 82 CHINESE *Determination of ERBB2 status: In the training set (55 samples), ERBB2 status was determined by conventional immunohistochemistry and in agreement with expression profiling. 21 are reported as ERBB2+. For other data sets, ERBB2 status was determined by expression profiling and analysis of ERBB2 and other 17q-linked genes.

Table S2: Classification Results of Independent Test and External Breast Cancer Datasets

Leave-One-Out Cross Validation (LOOCV): We used a standard leave-one-out cross-validation (LOOCV) approach to assess classification accuracy in the training set. In LOOCV, one sample in the training set is initially ‘left out’, and the classifier operations (eg gene selection and classifier training) are performed on the remaining samples. The ‘left out’ sample is then classified using the trained algorithm, and this process is then repeated for all samples in the training set.

The output of the WV analyses for all four data sets (including PS) and corresponding p-values for the association of ERBB2 expression with prediction confidence can be obtained as an Excel file from http://www.omniarray.com/ERClassification.html.

Table S3: Identification of Genes Important for ER Subtype Discrimination

Significance Analysis of Microarrays (SAM) was used to identify and rank 133 genes that were differentially regulated between ER+ and ER− tumors (FDR of 0%, ≧2-fold expression change). 122 of them are up-regulated in ER+(positive gene) and 11 are down-regulated in ER+ (negative genes). The S2N ratio of a particular gene reflects the extent of the expression perturbation observed between Low and High confidence samples.

TABLE S3 SAM-133 Gene List S2N Ratio Rank Probe_ID UG Gene Name GB_Accession ER− ER+ 122 Genes Positively Correlated to ER+ Status 1 205225_at Hs.1657 estrogen receptor 1 NM_000125.1 −0.29577 1.273725 2 209603_at Hs.169946 GATA-binding protein 3 AI796169_RC −1.08401 0.863193 3 204508_s_at Hs.279916 hypothetical protein FLJ20151 BC001012.1 −1.78617 0.608118 4 209604_s_at Hs.169946 GATA-binding protein 3 BC003070.1 −1.45575 0.776251 5 209602_s_at Hs.169946 GATA-binding protein 3 AI796169_RC −0.8137 0.654881 6 206754_s_at Hs.1360 cytochrome P450, subfamily IIB NM_000767.2 −0.2593 1.022511 (phenobarbital-Inducible), polypeptide 6 7 203963_at Hs.5338 carbonic anhydrase XII NM_001218.2 −1.46907 0.598453 8 214164_x_at Hs.5344 adaptor-related protein complex 1, BF752277 −1.38937 0.650127 gamma 1 subunit 9 212956_at Hs.90419 KIAA0882 protein AI348094_RC −0.64903 0.68526 10 215867_x_at Hs.5344 adaptor-related protein complex 1, AL050025.1 −1.63678 0.613887 gamma 1 subunit 11 210735_s_at Hs.5338 carbonic anhydrase XII BC000278.1 −1.44687 0.484214 12 214440_at Hs.155956 N-acetyltransferase 1 (arylamine N- NM_000662.1 −0.52605 1.043165 acetyltransferase) 13 202089_s_at Hs.79136 LIV-1 protein, estrogen regulated NM_012319.2 −0.61899 0.528173 14 210085_s_at Hs.279928 annexin A9 AF230929.1 −0.24463 1.123041 15 205862_at Hs.193914 KIAA0575 gene product NM_014668.1 −0.51927 0.883508 16 202088_at Hs.79136 LIV-1 protein, estrogen regulated AI635449_RC −0.5332 0.584697 17 211712_s_at Homo sapiens, clone MGC: 1925, BC005830.1 mRNA, complete cds. 18 206401_s_at Hs.101174 microtubule-associated protein tau J03778.1 −0.33797 0.700836 19 215304_at Hs.159264 Human clone 23948 mRNA sequence U79293.1 −0.52908 0.19541 20 218195_at Hs.15929 hypothetical protein FLJ12910 NM_024573.1 −0.62769 0.590894 21 212195_at Hs.71968 Homo sapiens mRNA; cDNA AL049265.1 −0.22898 0.854505 DKFZp564F053 (from clone DKFZp564F053) 22 203928_x_at Hs.101174 microtubule-associated protein tau AI870749_RC −0.35356 0.682993 23 209460_at Hs.283675 NPD009 protein AF237813.1 −0.18444 0.451265 24 212960_at Hs.90419 KIAA0882 protein BE646554_RC −0.58169 1.072165 25 209443_at Hs.76353 serine (or cysteine) proteinase inhibitor, J02639.1 0.065273 0.94045 clade A (alpha-1 antiproteinase, antitrypsin), member 5 26 209173_at Hs.91011 anterior gradient 2 (Xenepus laevis) AF088867.1 −0.80392 −0.25677 homolog 27 203071_at Hs.82222 sema domain, immunoglobulin domain NM_004636.1 −0.39014 0.726153 (Ig), short basic domain, secreted, (semaphorin) 3B 28 203571_s_at Hs.74120 adipose specific 2 NM_006829.1 −0.81429 0.240008 29 205354_at Hs.81131 guanidinoacetate N-methyltransferase NM_000156.3 −0.01557 0.074452 30 213712_at Hs.30504 Homo sapiens mRNA; cDNA BF508639_RC 0.008265 0.522867 DKFZp434E082 (from clone DKFZp434E082) 31 41660_at Cluster Incl. AL031588: dJ1163J1.1 (ortholog of mouse transmembrane receptor Celsr1 (KIAA0279 LIKE EGF-like domain containing protein similar to rat MEG 32 220744_s_at Hs.70202 WD repeat domain 10 NM_018262.1 −0.48046 0.159954 33 204798_at Hs.1334 v-myb avian myeloblastosis viral NM_005375.1 −0.46303 0.284211 oncogene homolog 34 215552_s_at Hs.272288 Human DNA sequence from clone RP1- AI073549_RC −0.19227 0.946801 63I5 on chromosome 6q25.1-26. Contains the 3 part of a novel gene and an exon of the ESR1 gene for estrogen receptor 1 (NR3A1, estradiol receptor), ESTs, STSs and GSSs 35 209339_at Hs.20191 seven in absentia (Drosophila) homolog 2 U76248.1 −0.0458 0.698282 36 210272_at Hs.330780 Human cytochrome P450-IIB (hIIB3) M29873.1 −0.58159 0.717949 mRNA, complete cds 37 205186_at Hs.33846 dynein, axonemal, light intermediate NM_003462.2 −0.49548 1.221071 polypeptide 38 207414_s_at Hs.170414 paired basic amino acid cleaving NM_002570.1 −0.00943 0.222009 system 4 39 205009_at Hs.1406 trefoil factor 1 (breast cancer, estrogen- NM_003225.1 −0.44277 0.213135 inducible sequence expressed in) 40 203628_at Hs.239176 insulin-like growth factor 1 receptor H05812_RC 0.241512 0.748503 41 211323_s_at Hs.198443 inositol 1,4,5-triphosphate receptor, L38019.1 −0.72886 0.116021 type 1 42 201825_s_at Hs.238126 CGI-49 protein AL572542_RC −0.32444 0.398111 43 211234_x_at Hs.1657 estrogen receptor 1 AF258449.1 0.268077 0.482442 44 209459_s_at Hs.283675 NPD009 protein AF237813.1 −0.40497 0.048419 45 212196_at Hs.71968 Homo sapiens mRNA; cDNA AW242916_RC −0.0843 0.516679 DKFZp564F053 (from clone DKFZp564F053) 46 203438_at Hs.155223 stanniocalcin 2 AI435828_RC −0.15925 0.456003 47 217838_s_at Hs.241471 RNB6 NM_016337.1 0.38602 0.872588 48 204041_at Hs.82163 monoamine oxidase B NM_000898.1 0.050799 0.120203 49 203929_s_at Hs.101174 microtubule-associated protein tau AI056359_RC −0.27747 0.427658 50 200670_at Hs.149923 X-box binding protein 1 NM_005080.1 −0.83621 0.279976 51 219414_at Hs.12079 calsyntenin-2 NM_022131.1 −0.47893 0.553864 52 203627_at Hs.239176 insulin-like growth factor 1 receptor AI830698_RC 0.088492 0.976305 53 208451_s_at Hs.278625 complement component 4B NM_000592.2 −0.42162 0.448767 54 213419_at Hs.324125 amyloid beta (A4) precursor protein- U62325.1 −0.01491 −0.06708 binding, family B, member 2 (Fe65-like) 55 205768_s_at Hs.11729 fatty-acid-Coenzyme A ligase, very NM_003645.1 −0.26778 0.41298 long-chain 1 56 204862_s_at Hs.81687 non-metastatic cells 3, protein NM_002513.1 −0.24568 0.320418 expressed in 57 210480_s_at Hs.22564 myosin VI U90236.2 −0.3344 −0.15111 58 205696_s_at Hs.105445 GDNF family receptor alpha 1 NM_005264.1 0.013863 0.846687 59 203685_at Hs.79241 B-cell CLLlymphoma 2 NM_000633.1 0.385651 0.915025 60 218976_at Hs.260720 J domain containing protein 1 NM_021800.1 −0.17876 0.280663 61 219197_s_at Hs.222399 CEGP1 protein AI424243_RC −0.09661 0.157384 62 202996_at Hs.82520 polymerase (DNA-directed), delta 4 NM_021173.1 0.158087 0.060137 63 205734_s_at Hs.38070 lymphoid nuclear protein related to AF4 AI990465_RC 0.187651 0.796703 64 211235_s_at Hs.1657 estrogen receptor 1 AF258450.1 0.269909 0.7271 65 211000_s_at Hs.82065 interleukin 6 signal transducer (gp130, AB015706.1 0.204138 0.785104 oncostatin M receptor) 66 217190_x_at Hs.247976 Estrogen receptor {exon 6} human, S67777 0.17102 0.653981 tamoxifen-resistant breast tumor 17, Genomic Mutant, 187 nt 67 202752_x_at Hs.22891 solute carrier family 7 (cationic amino NM_012244.1 −0.48423 0.153806 acid transporter, y+ system), member 8 68 201754_at Hs.74649 cytochrome c oxidase subunit VIc NM_004374.1 −0.79843 1.207003 69 204623_at Hs.82961 trefoil factor 3 (intestinal) NM_003226.1 −0.53903 0.149093 70 207038_at Hs.114924 solute carrier family 16 (monocarboxylic NM_004694.1 −0.50672 0.593732 acid transporters), member 6 71 212637_s_at Hs.324275 Homo sapiens mRNA; cDNA AU155187_RC −0.851 0.852788 DKFZp434D2111 (from clone DKFZp434D2111) 72 208682_s_at Hs.4943 hepatocellular carcinoma associated AF126181.1 −0.80969 −0.06845 protein; breast cancer associated gene 1 73 218502_s_at Hs.26102 trichorhinophalangeal syndrome I NM_014112.1 −0.26191 0.571226 74 202376_at Hs.234726 serine (or cysteine) proteinase inhibitor, NM_001085.2 0.02888 0.549323 clade A (alpha-1 antiproteinase, antitrypsin), member 3 75 215616_s_at Hs.301011 KIAA0876 protein AB020683.1 −0.00184 0.507129 76 211233_x_at Hs.1657 estrogen receptor 1 M12674.1 0.360947 0.949046 77 205081_at Hs.17409 cysteine-rich protein 1 (intestinal) NM_001311.1 −0.41153 −0.05483 78 214428_x_at Hs.170250 complement component 4A K02403.1 −0.22882 0.346824 79 209696_at Hs.574 fructose-1,6-bisphosphatase 1 D26054.1 −0.68072 0.137814 80 219682_s_at Hs.332150 TBX3-iso protein NM_016569.1 −0.26452 0.412502 81 212496_s_at Hs.301011 KIAA0876 protein BE256900 −0.272 0.841331 82 203108_at Hs.194691 retinoic acid induced 3 NM_003979.2 −0.51766 0.212322 83 206107_at Hs.65756 regulator of G-protein signalling 11 NM_003834.1 −0.0233 0.778074 84 218806_s_at Hs.267659 vav 3 oncogene AF118887.1 −0.3126 0.544105 85 209581_at Hs.37189 similar to rat HREV107 BC001387.1 −0.37261 0.359298 86 213412_at Hs.25527 tight junction protein 3 (zona occludens NM_014428.1 −0.76231 0.227893 3) 87 212638_s_at Hs.324275 Homo sapiens mRNA; cDNA BF131791 −0.76733 0.888627 DKFZp434D2111 (from clone DKFZp434D2111) 88 206469_x_at Hs.284236 aldo-keto reductase family 7, member NM_012067.1 −0.77705 0.278936 A3 (aflatoxin aldehyde reductase) 89 210652_s_at Hs.125783 DEME-6 protein BC004399.1 −0.29655 0.806265 90 216381_x_at Hs.284236 aldo-keto reductase family 7, member AL035413 −0.61275 0.253454 A3 (aflatoxin aldehyde reductase) 91 216092_s_at Hs.22891 solute carrier family 7 (cationic amino AL365347.1 −0.67193 0.152525 acid transporter, y+ system), member 8 92 208788_at Hs.250175 homolog of yeast long chain AL136939.1 −0.87121 0.346787 polyunsaturated fatty acid elongation enzyme 2 93 204792_s_at Hs.111862 KIAA0590 gene product NM_014714.1 0.085973 0.134751 94 207847_s_at Hs.89603 mucin 1, transmembrane NM_002456.1 −0.42941 −0.24975 95 213201_s_at Hs.73980 troponin T1, skeletal, slow AJ011712 −0.11892 0.71764 96 204497_at Hs.20196 adenylate cyclase 9 AB011092.1 0.007184 0.509774 97 222314_x_at Hs.205660 ESTs AW970881_RC −0.1322 0.201872 98 222212_s_at Hs.285976 tumor metastasis-suppressor AK001105.1 −0.74148 0.357607 99 219919_s_at Hs.279808 hypothetical protein FLJ10928 NM_018276.1 0.085456 0.152147 100 214053_at Hs.7888 Homo sapiens clone 23736 mRNA AW772192_RC −0.21533 0.32841 sequence 101 204934_s_at Hs.823 hepsin (transmembrane protease, NM_002151.1 −0.03851 0.743961 serine 1) 102 216109_at Hs.306803 Homo sapiens cDNA: FLJ21695 fis, AK025348.1 −0.03594 0.921802 clone COL09653 103 203749_s_at Hs.250505 retinoic acid receptor, alpha AI806984_RC −0.3159 1.006049 104 220329_s_at Hs.238270 hypothetical protein FLJ20627 NM_017909.1 0.068053 0.588123 105 204881_s_at Hs.152601 UDP-glucose ceramide NM_003358.1 −0.248 0.724338 glucosyltransferase 106 208305_at Hs.2905 progesterone receptor NM_000926.1 0.145722 0.687258 107 209623_at Hs.167531 methylcrotonoyl-Coenzyme A AW439494_RC −0.61293 0.369239 carboxylase 2 (beta) 108 218450_at Hs.108675 heme-binding protein NM_015987.1 −0.07982 0.486745 109 204343_at Hs.26630 ATP-binding cassette, sub-family A NM_001089.1 −0.36256 0.648789 (ABC1), member 3 110 219051_x_at Hs.124915 hypothetical protein MGC2601 NM_024042.1 −0.43578 0.112222 111 205471_s_at Hs.63931 dachshund (Drosophila) homolog AW772082_RC −0.43168 −0.26408 112 203439_s_at Hs.155223 stanniocalcin 2 BC000658.1 −0.28836 0.67174 113 204863_s_at Hs.82065 Interleukin 6 signal transducer (gp130, BE856546_RC 0.259289 0.691633 oncostatin M receptor) 114 203289_s_at Hs.19699 Conserved gene telomeric to alpha BE791629 −0.18036 0.122646 globin cluster 115 221765_at Hs.23703 ESTs AI378044_RC −0.0539 0.714017 116 219001_s_at Hs.317589 hypothetical protein MGC10765 NM_024345.1 −0.28755 0.64098 117 220581_at Hs.287738 hypothetical protein FLJ23305 NM_025059.1 −0.13763 0.781039 118 211596_s_at Homo sapiens mRNA for membrane AB050468.1 glycoprotein LIG-1, complete cds. 119 205645_at Hs.80667 RALBP1 associated Eps domain NM_004726.1 −0.29164 0.308819 containing 2 120 219663_s_at Hs.157527 hypothetical protein MGC4659 NM_025268.1 0.059072 −0.06016 121 205380_at Hs.15456 PDZ domain containing 1 NM_002614.1 0.094959 0.486972 122 201508_at Hs.1516 insulin-like growth factor-binding protein 4 NM_001552.1 0.102433 0.237825 11 Genes Negatively Correlated to ER+ Status 1 215729_s_at Hs.9030 TONDU BE542323 0.729732 −0.40161 2 201983_s_at Hs.77432 epldermal growth factor receptor (avian AW157070_RC 0.183968 −0.10873 erythroblastic leukemia viral (v-erb-b) oncogene homolog) 3 204914_s_at Hs.32964 SRY (sex determining region Y)-box 11 AW157202_RC −0.3552 −0.61822 4 204913_s_at Hs.32964 SRY (sex determining region Y)-box 11 AI360875_RC −0.54222 −0.6594 5 205646_s_at Hs.89506 paired box gene 6 (aniridia, keratitis) NM_000280.1 0.667994 −0.15217 6 207030_s_at Hs.10526 cysteine and glycine-rich protein 2 NM_001321.1 0.526203 −0.44193 7 204915_s_at Hs.32964 SRY (sex determining region Y)-box 11 AB028641.1 −0.4419 −0.47414 8 203021_at Hs.251754 secretory leukocyte protease inhibitor NM_003064.1 −0.08293 −1.00559 (antileukoproteinase) 9 209800_at Hs.115947 keratin 16 (focal non-epidermolytic AF061812.1 0.573263 −0.29962 palmoplantar keratoderma) 10 203234_at Hs.77573 uridine phosphorylase NM_003364.1 0.30456 0.307505 11 201984_s_at Hs.77432 epldermal growth factor receptor (avian NM_005228.1 0.416409 0.086073 erythroblastic leukemia viral (v-erb-b) oncogene homolog)

Top 54 ER Discriminating Genes that are Negatively Correlated to ER+ Status

Due to the limited number of ER negative genes, we decreased the threshold of SAM to derive 54 genes with FDR of 0%. These negative genes were used in FIG. 2 c) and d).

Table S4: Comparing the Global Expression Profiles of ‘High’ and ‘Low-Confidence’ Tumors

SAM was used to identify differentially regulated genes between a) ER+ ‘High’ and ‘Low’ Confidence tumors, and b) ER− ‘High’ and ‘Low’ Confidence tumors. For the ER+ comparison, 50 genes were identified as up-regulated in ER+/Low and 39 are downregulated in comparison to ER+/High tumors. For the ER− comparison, 50 genes were identified as up-regulated in ER−/Low, and no genes were identified as being downregulated in comparison to ER−/High tumors.

TABLE S4 Top-ranked genes differently expressed in Low/High confidence samples UniGene Rank Chromosome a) ER+/Low vs. ER+/High Genes Up-regulated in ER+/Low chloride channel, calcium activated, family member 2 Hs.241551 1 ESTs, Weakly similar to hypothetical protein H. sapiens Hs.106642 2 v-myc avian myelocytomatosis viral related oncogene, neuroblastoma Hs.25960 3 derived phenylethanolamine N-methyltransferase Hs.1892 4 17q21-q22 Alu-binding protein with zinc finger domain Hs.289104 5 fibroblast growth factor receptor 4 Hs.165950 6 KIAA0300 protein Hs.173035 7 growth factor receptor-bound protein 7 Hs.86859 8 17q21.1 myosin, heavy polypeptide 4, skeletal muscle Hs.272207 9 apomucin Hs.103707 10 proline oxidase homolog Hs.274550 11 S100 calcium-binding protein AB (calgranulin A) Hs.100000 12 glycine C-acelyltransferase (2-amino-3-ketobutyrate coenzyme A Hs.54609 13 ligase) phospholamban Hs.85050 14 CGI-96 protein Hs.239934 15 leptin (murine obesity homolog) Hs.194236 16 hypothetical protein FLJ14146 Hs.103395 17 kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) Hs.107318 18 Inhibin, beta B (activin AB beta polypeptide) Hs.1735 19 hydroxysteroid (17-beta) dehydrogenase 2 Hs.155109 20 fatty acid binding protein 7, brain Hs.26770 21 orosomucoid 2 Hs.278388 22 secretory leukocyte protease inhibitor (antileukoproteinase) Hs.251754 23 actin, gamma 2, smooth muscle, enteric Hs.78045 24 Homo sapiens mRNA; cDNA DKFZp564G112 (from clone Hs.51515 25 DKEp564G112) peptidylarginine delminase type III Hs.149195 26 myosin, heavy polypeptide 11, smooth muscle Hs.78344 27 S100 calcium-binding protein A9 (calgranulin B) Hs.112405 28 Homo sapiens clone 23809 mRNA sequence Hs.6932 29 integrin, beta 6 Hs.123125 30 lipopolysaccharide-binding protein Hs.154078 31 glutamate receptor, lonotrophic, AMPA 3 Hs.100014 32 Homo sapiens PAC clone RP5-1093O17 from 7q11.23-q21 Hs.193606 33 KIAA1102 protein Hs.202949 34 transmembrane 4 superfamily member 3 Hs.84072 35 v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 Hs.323910 36 17q11.2-q12 (neuroglioblastoma derived oncogene homolog) protein phosphatase 1, regulatory (inhibitor) subunit 1A Hs.76780 37 HGC6.1.1 protein Hs.225962 38 mucin and cadherin-like Hs.165619 39 homeo box A9 Hs.127428 40 4-hydroxyphenylpyruvate dioxygenase Hs.2899 41 lactotransferrin Hs.105938 42 KIAA1069 protein Hs.193143 43 folate hydrolase (prostate-specific membrane antigen) 1 Hs.1915 44 argininosuccinate synthetase Hs.160786 45 keratin 7 Hs.23881 46 angiotensin receptor 2 Hs.3110 47 calmodulin-like skin protein Hs.180142 48 electron-transfer-flavoprotein, alpha polypeptide (glutaric aciduria II) Hs.169919 49 S100 calcium-binding protein A7 (psoriasin 1) Hs.112408 50 Genes Down-regulated in ER+/Low phorbol-12-myristate-13-acetate-induced protein 1 Hs.96 1 dynein, axonemal, light intermediate polypeptide Hs.33846 2 cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6 Hs.1360 3 estrogen receptor 1 Hs.1657 4 artemin Hs.194689 5 carcinoembryonic antigen-related cell adhesion molecule 1 (biliary Hs.50964 6 glycoprotein) ESTs Hs.23703 7 KIAA0575 gene product Hs.193914 8 retinoic acid receptor, alpha Hs.250505 9 annexin A9 Hs.279928 10 Cas-B_(F) M (murine) ectropic retroviral transforming sequence c Hs.156637 11 GATA-binding protein 3 Hs.169946 12 hypothetical protein FLJ12650 Hs.4243 13 arsenate resistance protein ARS2 Hs.111801 14 huntingtin interacting protein 2 Hs.155485 15 hypothetical protein FLJ13134 Hs.99603 16 zinc finger protein 165 Hs.55481 17 Homo sapiens cDNA: FLJ21695 fis, clone COL09653 Hs.306803 18 insulin-like growth factor 1 receptor Hs.239176 19 hepsin (transmembrane protease, serine 1) Hs.823 20 two pore potassium channel KT3.3 Hs.203845 21 UDP-glucose ceramide glucosyltransferase Hs.152601 22 Human cytochrome P450-IIB (hIIB3) mRNA, complete cds Hs.330780 23 sema domain, immunoglobulin domain (Ig). short basic domain, Hs.32981 24 secreted, (semaphorin) 3F microtubule-associated protein tau Hs.101174 25 phosphatidylserine-specific phospholipase A1alpha Hs.17752 26 Similar to hypothetical protein PRO2831 [Homo sapiens], mRNA Hs.406646 27 sequence cytochrome c oxidase subunit VIc Hs.74649 28 adenylate cyclase 9 Hs.20196 29 Homo sapiens cytokine-like nuclear factor n-pac mRNA, complete Hs.331584 30 cds Human DNA sequence from clone RP1-63I5 on chromosome Hs.272288 31 6q25.1-26. Contains the 3 part of a novel gene and an exon of the ESR1 gene for estrogen receptor 1 (NR3A1, estradiol receptor). ESTs, STSs and GSSs calsyntenin-2 Hs.12079 32 interleukin 6 signal transducer (gp130, oncostatin M receptor) Hs.82065 33 A kinase (PRKA) anchor protein 10 Hs.75456 34 N-acetyltransferase 1 (arylamine N-acetyltransferase) Hs.155956 35 hypothetical protein FLJ13687 Hs.278850 36 cystatin SA Hs.247955 37 heat shock 27 kD protein 1 Hs.76067 38 synaptojanin 2 Hs.61289 39 b) ER−/Low vs. ER−/High Genes Up-regulated in ER/Low UDP-N-acetyl-alpha-D-galactosamine:polypeptide N- Hs.151678 1 acetylgalactosaminyltransferase 6 (GalNAc-T6) aldehyde dehydrogenase 4 family, member A1 Hs.77448 2 chromosome 6 open reading frame 29 Hs.334514 3 melanoma antigen, family D, 2 Hs.4943 4 phenylethanolamine N-methyltransferase Hs.1892 5 17q21-q22 tripartite motif-containing 3 Hs.321576 6 hypothetical gene MGC9753 Hs.91668 7 ATP-binding cassette, sub-family C (CFTR/MRP), member 6 Hs.274260 8 SH3 domain binding glutamic acid-rich protein like Hs.14368 9 growth factor receptor-bound protein 7 Hs.86859 10 17q21.1 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial) Hs.59889 11 fibroblast growth factor receptor 4 Hs.165950 12 fatty acid synthase Hs.83190 13 mucin 1, transmembrane Hs.89603 14 phafin 2 Hs.29724 15 carnitine acetyltransferase Hs.12068 16 hypothetical protein FLJ20151 Hs.279916 17 GATA binding protein 3 Hs.169946 18 WW domain-containing protein 1 Hs.355977 19 transcription factor AP-2 beta (activating enhancer binding protein 2 Hs.33102 20 beta) KIAA0882 protein Hs.90419 21 tetraspan 1 Hs.38972 22 peroxisomal biogenesis factor 11A Hs.31034 23 solute carrier family 4, sodium bicarbonate cotransporter, member 8 Hs.132136 24 hypothetical gene MGC9753 Hs.91668 25 forkhead box A1 Hs.70604 26 aquaporin 3 Hs.234642 27 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, Hs.323910 28 17q11.2-q12 neuro/glioblastoma derived oncogene homolog (avian) inositol 1,4,5-triphosphate receptor, type 1 Hs.198443 29 hypothetical protein PRO1489 Hs.197922 30 aldehyde dehydrogenase 3 family, member B2 Hs.87539 31 Hypothetical protein [Homo sapiens], mRNA sequence Hs.381412 32 dual specificity phosphatase 6 Hs.180383 33 carbonic anhydrase XII Hs.5338 34 NAD(P)H dehydrogenase, quinone 1 Hs.406515 35 mannosidase, alpha, class 1C, member 1 Hs.8910 36 KIAA0703 gene product Hs.6168 37 stearoyl-CoA desaturase (delta-9-desaturase) Hs.119597 38 fructose-1,6-bisphosphatase 1 Hs.574 39 arylsulfatase D Hs.326525 40 X-box binding protein 1 Hs.149923 41 methylcrotonoyl-Coenzyme A carboxylase 2 (beta) Hs.167531 42 synaptosomal-associated protein, 23 kDa Hs.184376 43 kraken-like Hs.301947 44 anterior gradient 2 homolog (Xenepus laevis) Hs.91011 45 hypothetical protein FLJ20174 Hs.114556 46 chaperonin containing TCP1, subunit 2 (beta) Hs.432970 47 immunoglobulin heavy constant gamma 3 (G3m marker) Hs.300697 48 transmembrane 4 superfamily member 3 Hs.84072 49 sorbitol dehydrogenase Hs.878 50

Use of DRAGON-ERE Finder (DEREF) to Identify Putative EREs in Gene Promoters

The DEREF algorithm was used to define potential EREs in the promoters of genes belonging to various categories (see http://sdmc.lit.org.sg/ERE-V2/index for a description of the underlying methodology of DEREF). The manuscript of ref. 14 can be accessed via http://www.omniarray.com/ERClassification.html. The estrogen-induced SAGE data set was derived from (http://143.111.133.249/ggeg/, see ref. 13), using the thresholds of 3 hr fold increase >=2 and 3 hr p value <0.005. 65 SAGE Tags were selected. These 65 SAGE Tags matched 68 genes that are furthered subject to ERE analysis. The gene set of the top 100 genes negatively correlated to ER status was derived using SAM. Table S6a depicts the results.

TABLE S6a The ERE prediction on various data sets: E2-induced SAGE data set, genes negatively correlated to ER+, and the SAM-133 gene set. ERE Hit with high Data set Non-ERE Low High confidence ‘N/A’ SAGE E2-induced 21 15 21 41.18% 11 ER-negative genes 50 22 6 7.69% 22 SAM-133 15 15 17 36.17% 23

TABLE S6b Predicted ERE patterns by DEREF for genes listed in Table 2 of the main text. ERE pattern for Table 2 Gene Name Rank ERE pattern 12 ERE with high confidence out of 50 genes perturbed in ER+ annexin A9 4 PP 2783 CA-GGGCA-CCC-CAGCC-TG new CCTGTTGGGGCACATACCAGCAGGGCACCCCAGCCT GCACCCCAGAGGGGGTCCCAG 21 N-acetyltransferase 1 (arylamine N- 5 PP 150 AA-GGTTA-CAA-TAACC-AA new acetyltransferase) CCACCTTCAAATCATACTACAAGGTTACAATAACCAA AACAGCGTGGTACTGATACA 21 retinoic acid receptor, alpha 7 PP 2149 GA-GGTCC-CTC-TGCCC-CT new TGAAGTTGATCTGTTGTATTGAGGTCCCTCTGCCCCT ATATTTATCCTAAATGGTAT 21 B-cell CLL/lymphoma 2 11 PP 647 CA-GGGCA-CAG-TGGCT-CA new GACAAAATAAAGATGTCAGGCAGGGCACAGTGGCTC ATGTCTGTAATCCCAGCACTT 21 RNB6 13 PP 1920 TT-GGTCA-GGC-TGGTC-TC known AAAGACAGGGTTTCACCATGTTGGTCAGGCTGGTCT CGAACTTCTGACCTCAGGTGA 21 regulator of G-protein signalling 11 21 PP 847 CG-GGTCA-CTG-CAACC-TC new GGAGTGCAATGGTGCAATCTCGGGTCACTGCAACCT CCGCCTCCTGGGTTCAAGCGA 21 UDP-glucose ceramide 25 PP 466 TG-AGTCA-CCG-TGCCC-AG new glucosyltransferase AAGTGCTGGGATTACAGGCGTGAGTCACCGTGCCCA GCCAATGGCTTGTGGTTTTCT 21 ATP-binding cassette, sub-family A 33 PP 1363 CA-GGGCA-CAG-TGGCT-CA new (ABC1), member 3 GCACAGAGATAAAACCTCGGCAGGGCACAGTGGCTC ACGCCTGTAATCCCCACACTT 21 carbonic anhydrase XII 34 PP 1376 TA-GGCCA-AAC-TAACC-TT new TCCTTATTCATTCCTGGGCATAGGCCAAACTAACCTT AGAAAGGAATTCAGTTTATG 21 serine (or cysteine) proteinase 40 PP 2408 TT-GGTCG-GAC-TGGTC-TT new inhibitor, clade A (alpha-1 AGAGACAGGGTTTCACCTTGTTGGTCGGACTGGTCT antiproteinase, antitrypsin), member 3 TGAACTCCTGACCTCGTGATC 21 adenylate cyclase 9 44 PP 710 TT-GGTCA-GGC-TGGTC-TC known AGAGATGGGGTTTCTCCGTGTTGGTCAGGCTGGTCT CGAACTCCCGACCTCAGGTGA 21 heme binding protein 1 46 PP 1738 GA-GGTCC-GGG-TGGCC-GC new AAAGAGCAGAGGCGCCCGTAGAGGTCCGGGTGGCC GCTGCTGTTAACATCCATCACT 21 3 ERE with high confidence out of 50 genes perturbed in ER− LAG1 longevity assurance homolog 2 13 PP 3662 CA-GGCCA-GGG-CAAGC-CC new (S. cerevisiae) CCCAAGCCACAGGACGCGTCCAGGCCAGGGCAACC CCGCGGGCCGCTGCCAGGGTGG 21 fructose-1,6-bisphosphatase 1 15 PP 776 TT-GGTCA-GGC-TGGTC-TC known AGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCT CGAGCTCCCAACCTCAGGTGA 21 hypothetical protein MGC2601 33 PP 966 CT-GGTCA-GGC-TGGTC-TT new AGAGACGAGGTTTCTCCATGCTGGTCAGGCTGGTCT TGAACTCCCGACCTCAGGTGA 21

e S7: Weighted Voting parameters for mean (μ) and standard deviation (σ) of expression data

SAM-133 geneset ER− ER+

_ID Gene Name mean SD mean SD

0_at X-box binding protein 1 0.786506 0.716285 4.265411 1.422852

8_at insulin-like growth factor-binding protein 4 −0.34357 1.388805 2.57045 0.925761

4_at cytochrome c oxidase subunit VIc −1.58027 1.870693 1.927493 1.237708

5_s_at CGI-49 protein 3.371655 1.153737 5.720964 0.582412

3_s_at epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) −0.23687 1.75591 2.753161 0.803569 oncogene homolog)

4_s_at epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) −1.44281 0.960058 2.42027 2.337701 oncogene homolog)

8_at LIV-1 protein, estrogen regulated 1.312524 1.221556 3.870357 0.929939

9_s_at LIV-1 protein, estrogen regulated 1.734565 1.093064 4.085214 0.81537

6_at serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), 2.023548 1.032196 4.420661 0.934515 member 3

2_x_at solute carrier family 7 (cationic amino acid transporter, y+ system), member 8 1.981605 1.049118 4.149982 0.712426

6_at polymerase (DNA-directed), delta 4 0.786499 1.029001 3.014232 0.865812

1_at secretory leukocyte protease inhibitor (antileukoproteinase) 0.355523 0.675879 3.16287 1.761351

1_at sema domain, immunoglobulin domain (Ig), short basic domain, secreted, 1.825558 0.726706 4.052804 1.145816 (semaphorin) 3B

8_at retinoic acid induced 3 −2.75146 0.887259 −0.09227 1.606679

4_at uridine phosphorylase −2.68964 1.552946 0.243702 1.641435

9_s_at Conserved gene telomeric to alpha globin cluster 3.20195 0.718557 5.197518 0.987453

8_at stanniocalcin 2 −1.29648 1.055361 0.795528 0.993152

9_s_at stanniocalcin 2 −1.57332 1.345545 0.998514 1.454402

1_s_at adipose specific 2 0.233895 0.988328 2.283714 1.060332

7_at insulin-like growth factor 1 receptor 0.141016 0.610073 2.127288 1.174363

8_at insulin-like growth factor 1 receptor 2.29995 0.509475 3.833107 0.788714

5_at B-cell CLLlymphoma 2 −1.10751 1.324287 1.15701 1.355875

9_s_at retinoic acid receptor, alpha −1.58118 1.167735 0.537334 1.268906

8_x_at microtubule-associated protein tau 0.359852 0.516477 1.888305 0.821962

9_s_at microtubule-associated protein tau −2.59884 0.565755 −0.00962 2.145673

3_at carbonic anhydrase XII 1.190756 3.229512 4.402 1.181501

1_at monoamine oxidase B −3.13061 1.085626 −0.75919 1.755041

3_at ATP-binding cassette, sub-family A (ABC1), member 3 −0.29571 1.843682 2.228971 1.512369

7_at adenylate cyclase 9 −2.34613 1.534418 −0.05573 1.429526

8_s_at hypothetical protein FLJ20151 −3.52135 1.303031 −0.87495 2.10528

3_at trefoil factor 3 (intestinal) −0.37083 1.33889 1.50405 0.899477

2_s_at KIAA0590 gene product −0.9475 1.745737 1.257564 1.170708

8_at v-myb avian myeloblastosis viral oncogene homolog 1.288571 1.107004 3.060625 0.97928

2_s_at non-metastatic cells 3, protein expressed in −1.44821 0.786716 0.388854 1.271171

3_s_at interleukin 6 signal transducer (gp130, oncostatin M receptor) −0.10956 1.179102 1.970259 1.431009

1_s_at UDP-glucose ceramide glucosyltransferase −1.39262 1.195462 1.156751 2.153286

3_s_at SRY (sex determining region Y)-box 11 −2.53383 1.536914 −0.16571 1.727001

4_s_at SRY (sex determining region Y)-box 11 −1.8799 1.273909 0.144791 1.375233

5_s_at SRY (sex determining region Y)-box 11 0.484505 1.125341 2.823356 1.941558

4_s_at hepsin (transmembrane protease, serine 1) 0.462278 0.985428 2.501289 1.570414

9_at trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in) −1.98675 1.39922 −0.14861 0.959657

1_at cysteine-rich protein 1 (intestinal) 0.366598 1.124549 1.87895 0.590829

6_at dynein, axonemal, light intermediate polypeptide −2.39302 0.959482 −0.48343 1.433455

5_at estrogen receptor 1 −1.62943 1.558096 0.486988 1.459551

4_at guanidinoacetate N-methyltransferase 0.719039 0.547264 2.096279 0.868384

0_at PDZ domain containing 1 −0.92507 1.254295 1.252606 1.789471

1_s_at dachshund (Drosophila) homolog 1.676963 0.591793 3.169036 1.05951

5_at RALBP1 associated Eps domain containing 2 −0.63258 1.838056 2.053427 2.368533

6_s_at paired box gene 6 (aniridia, keratitis) −0.06075 0.836545 1.524428 1.119938

6_s_at GDNF family receptor alpha 1 3.8834 1.041947 5.212661 0.43379

4_s_at lymphoid nuclear protein related to AF4 −1.3702 1.00987 0.420671 1.393757

8_s_at fatty-acid-Coenzyme A ligase, very long-chain 1 0.5008 0.790296 2.069968 1.166292

2_at KIAA0575 gene product 2.848348 1.291904 4.670661 1.303459

7_at regulator of G-protein signalling 11 −1.36697 1.337414 0.179662 0.681822

1_s_at microtubule-associated protein tau −3.3514 1.637863 −1.01214 2.020108

9_x_at aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase) 0.948475 0.99349 2.289914 0.621401

4_s_at cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6 −0.71324 1.775643 1.082716 0.869708 207030_s_at cysteine and glycine-rich protein 2 −2.03214 1.126525 −0.19338 1.540646 207038_at solute carrier family 16 (monocarboxylic acid transporters), member 6 0.374876 0.580637 1.790818 1.094049 207414_s_at paired basic amino acid cleaving system 4 0.341324 1.065353 2.062852 1.376036 207847_s_at mucin 1, transmembrane 0.247008 1.354516 2.257601 1.737215 208305_at progesterone receptor −1.24605 0.974745 0.384022 1.29497 208451_s_at complement component 4B −4.78762 1.049086 −2.66361 2.080728 208682_s_at hepatocellular carcinoma associated protein; breast cancer associated gene 1 −1.959 0.821013 −0.3239 1.382716 208788_at homolog of yeast long chain polyunsaturated fatty acid elongation enzyme 2 0.152008 0.660975 1.523099 1.038038 209173_at anterior gradient 2 (Xenepus laevis) homolog −4.28803 0.661578 −2.56017 1.677193 209339_at seven in absentia (Drosophila) homolog 2 1.270858 1.066389 2.646046 0.849767 209443_at serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), 4.667825 0.671724 5.873446 0.804606 member 5 209459_s_at NPD009 protein 1.072112 1.457092 2.973341 1.645057 209460_at NPD009 protein −0.96002 1.349904 0.607753 1.04472 209581_at similar to rat HREV107 −0.56188 0.872894 0.668399 0.727131 209602_s_at GATA-binding protein 3 2.019065 1.056594 3.416464 0.940078 209603_at GATA-binding protein 3 1.985985 0.863569 3.186089 0.674166 209604_s_at GATA-binding protein 3 2.395052 1.790175 4.34208 1.519527 209623_at methylcrotonoyl-Coenzyme A carboxylase 2 (beta) −1.00419 1.154041 0.445889 1.017354 209696_at fructose-1,6-bisphosphatase 1 −1.68104 0.963742 −0.1215 1.377052 209800_at keratin 16 (focal non-epidermolytic palmoplantar keratoderma) 2.324715 1.562155 4.012295 1.229197 210085_s_at annexin A9 2.4829 1.125042 4.043161 1.290489 210272_at Human cytochrome P450-IIB (hIIB3) mRNA, complete cds 1.01495 0.91653 2.191543 0.64021 210480_s_at myosin VI −0.14392 1.616287 1.455335 1.006298 210652_s_at DEME-6 protein 1.251577 0.889677 2.556116 0.970199 210735_s_at carbonic anhydrase XII 1.213425 2.03426 3.084783 1.272118 211000_s_at interleukin 6 signal transducer (gp130, oncostatin M receptor) −3.02427 1.43442 −1.18813 1.697067 211233_x_at estrogen receptor 1 −0.0459 1.740133 1.544577 0.867934 211234_x_at estrogen receptor 1 0.044649 1.763802 1.765441 1.206805 211235_s_at estrogen receptor 1 −2.24335 1.765844 −0.48324 1.306074 211323_s_at inositol 1,4,5-triphosphate receptor, type 1 2.749775 0.789763 3.855643 0.652063 211596_s_at Homo sapiens mRNA for membrane glycoprotein LIG-1, complete cds. 0.451307 1.03825 1.691284 0.751559 211712_s_at Homo sapiens, clone MGC: 1925, mRNA, complete cds. 0.615955 1.516076 2.069047 0.790366 212195_at Homo sapiens mRNA; cDNA DKFZp564F053 (from clone DKFZp564F053) 0.66476 0.873729 1.797193 0.663081 212196_at Homo sapiens mRNA; cDNA DKFZp564F053 (from clone DKFZp564F053) 1.370605 0.637597 2.49272 0.820267 212496_s_at KIAA0876 protein 2.9339 0.874367 4.097768 0.756001 212637_s_at Homo sapiens mRNA; cDNA DKFZp434D2111 (from clone DKFZp434D2111) −1.88266 1.081913 −0.63578 0.780821 212638_s_at Homo sapiens mRNA; cDNA DKFZp434D2111 (from clone DKFZp434D2111) 2.261515 1.394089 3.785398 1.192581 212956_at KIAA0882 protein −2.7829 1.397052 −0.86347 2.046812 212960_at KIAA0882 protein −0.50333 1.45485 0.947772 1.02444 213201_s_at troponin T1, skeletal, slow −1.9544 1.210569 −0.40381 1.441706 213412_at tight junction protein 3 (zona occludens 3) 2.951875 0.714379 4.007446 0.711117 213419_at amyloid beta (A4) precursor protein-binding, family B, member 2 (Fe65-like) −2.21361 1.478023 −0.51415 1.591816 213712_at Homo sapiens mRNA; cDNA DKFZp434E082 (from clone DKFZp434E082) 0.270749 0.847277 1.499404 1.020576 214053_at Homo sapiens clone 23736 mRNA sequence −0.39205 1.186238 0.845048 0.820314 214164_x_at adaptor-related protein complex 1, gamma 1 subunit −1.08541 1.111223 0.178117 0.95879 214428_x_at complement component 4A 0.533406 0.838849 1.642348 0.807099 214440_at N-acetyltransferase 1 (arylamine N-acetyltransferase) −0.99962 0.684062 0.154358 0.999297 215304_at Human clone 23948 mRNA sequence 2.4353 0.529481 3.488893 0.879103 215552_s_at Human DNA sequence from clone RP1-63I5 on chromosome 6q25.1-26. Contains the −4.0518 1.024367 −2.20072 2.254477 3 part of a novel gene and an exon of the ESR1 gene for estrogen receptor 1 (NR3A1, estradiol receptor), ESTs, STSs and GSSs 215616_s_at KIAA0876 protein 2.582125 0.659442 3.570411 0.700552 215729_s_at TONDU 1.641575 0.849076 2.756482 0.863148 215867_x_at adaptor-related protein complex 1, gamma 1 subunit −0.42352 0.884606 0.727052 0.926142 216092_s_at solute carrier family 7 (cationic amino acid transporter, y+ system), member 8 0.063651 1.352604 1.366287 0.918248 216109_at Homo sapiens cDNA: FLJ21695 fis, clone COL09653 −1.17386 1.143511 0.232514 1.345207 216381_x_at aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase) 0.46636 0.383625 1.657506 1.251032 217190_x_at Estrogen receptor {exon 6} human, tamoxifen-resistant breast tumor 17, 0.899139 0.533766 2.030393 1.097631 Genomic Mutant, 187 nt 217838_s_at RNB6 −1.31066 0.930532 −0.16453 0.933916 218195_at hypothetical protein FLJ12910 0.847629 0.786234 2.077682 1.202885 218450_at heme-binding protein 0.080843 0.82158 1.234993 1.027254 218502_s_at trichorhinophalangeal syndrome I −1.57325 1.012703 −0.27651 1.276184 218806_s_at vav 3 oncogene 1.662298 0.790643 2.689179 0.799202 218976_at J domain containing protein 1 −1.84709 1.306292 −0.43267 1.374615 219001_s_at hypothetical protein MGC10765 −2.18314 1.146729 −0.93169 1.100879 219051_x_at hypothetical protein MGC2601 −1.64776 1.079359 −0.04531 1.917545 219197_s_at CEGP1 protein 3.017955 0.866409 4.110571 0.929583 219414_at calsyntenin-2 219663_s_at hypothetical protein MGC4659 219682_s_at TBX3-iso protein −2.31967 2.774285 −5.24093 1.743328 219919_s_at hypothetical protein FLJ10928 1.5957 1.348698 −0.22476 1.003375 220329_s_at hypothetical protein FLJ20627 1.476165 1.643622 −0.81183 1.617203 220581_at hypothetical protein FLJ23305 0.707923 1.691725 −1.11592 1.188481 220744_s_at WD repeat domain 10 −1.15664 1.569856 −2.79242 0.859538 221765_at ESTs 1.266316 0.936218 −0.08462 0.892242 222212_s_at tumor metastasis-suppressor 0.105187 1.541242 −1.65582 1.335109 222314_x_at ESTs 2.914925 1.476344 1.290308 1.093452 41660_at Cluster Incl. AL031588:dJ1163J1.1 (ortholog of mouse transmembrane receptor Celsr1 −1.50101 2.986928 −3.88453 1.411412 (KIAA0279 LIKE EGF-like domain containing protein similar to rat MEG −0.50993 0.923661 −1.93244 1.140847 0.987597 0.893199 −0.11725 0.498882

indicates data missing or illegible when filed

TABLE S8 Gene Expression data for Genes of Table A4 (common-13 genes) UID NAME 2000683T+neg 2000775T+neg 2000804T+neg 980346T+pos 980383T+neg 990082T+neg 980177T+neg 980178T+neg 980403T+neg 980434T+neg 990075T+neg 990113T+neg 990107T+neg 980203T+neg 980208T+pos 980220T+pos 980221T+neg 990115T+pos 990375T+neg 980404T+neg 980409T+neg 990123T+neg 2000422T+neg 2000787T-LA 2000818T-LA 20020021T-LA 20020051T-LA 20020056T-LA 980197T+pos 980215T+neg 980217T+neg 980261T+neg 980391T+neg 2000768T+pos 2000779T+neg 2000948T+neg 20020160T-LA 2000401T-LA 20020071T-LA 2000215T-normal-like 2000220T-LA 980333T-LA 980058T-LA 980278T-LA 980288T-ERBB2 2000597T-LA 2000609T-LA 2000272T-LA 2000274T-normal-like 980285T-Basal 2000593T-Basal 2000638T-Basal 2000641T-ERBB2 2000675T-ERBB2 2000287T-ERBB2 2000320T-Basal 2000880T-Basal 2000731T-Basal 980353T−neg 2000829T−pos 980373T−pos 2000500T−neg 2000759T−pos 980238T−pos 980395T−pos 980396T−pos 980411T−neg 980441T−neg 990262T−neg 980216T−neg 980194T−pos 980247T−pos 980338T−neg 990174T−neg 990299T−neg 2000210T-ERBB2 980315T-LA 980335T-ERBB2 980193T-Basal 980256T-Basal 980214T+pos 990148T+pos 2000209T+pos 990223T+pos 2000104T-ERBB2 2000651T-normal-like 2000237T-ERBB2 2000652T-ERBB2 2000376T-ERBB2 2000399T-ERBB2 20020090T-ERBB2 2000709T-ERBB2 2000813T−pos 980380T−pos 990134T−pos 2000171T-ERBB2 Confidence High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High High Low Low Low Low Low Low Low Low Low Low Low Low Low Low Low Low 201525_at apolipoprotein D 2.749 7.332 2.111 2.803 1.752 1.958 1.75 2.712 4.541 3.009 3.613 4.291 1.486 4.204 2.849 3.388 3.262 3.603 3.097 7.419 5.491 4.873 1.444 2.954 1.296 3.352 2.856 2.266 5.145 4.695 4.072 6.963 4.804 2.886 0.7888 3.226 0.3389 1.921 2.803 4.261 4.993 4.251 0.785 6.066 4.539 2.019 5.235 1.808 4.592 0.09904 2.77 2.85 3.059 3.353 1.229 1.679 1.879 2.77 0.9126 4.246 6.957 3.753 7.109 4.31 1.624 2.986 2.603 0.984 4.797 0.5836 5.433 2.722 1.66 3.161 2.94 0.3395 1.008 4.023 2.417 4.21 4.833 5.118 0.7322 7.893 5.443 5.369 1.104 6.198 2.819 3.773 1.536 1.673 6.562 4.973 6.796 6.121 202991_at START domain containing 3 0.1623 0.7959 −0.3925 3.014 0.4513 0.2522 0.3208 −0.2599 0.5714 −0.5644 0.5246 0.8061 0.6035 −0.3416 2.886 0.8943 −0.6905 2.991 0.6204 0.4511 −0.4408 −0.2534 0.07863 1.517 0.6792 0.6636 0.2455 −0.1443 2.871 −0.3209 −0.05486 1.605 0.1314 2.252 0.002929 0.9972 0.08306 2.623 0.4914 0.4794 −0.02506 0.1142 0.3137 0.5399 3.005 0.2001 2.758 0.1815 0.1945 −0.05305 0.6643 0.5267 2.002 0.462 3.014 0.2885 0.1389 −0.05295 −1.923 1.882 0.5175 0.09324 1.667 3.328 2.384 3.651 1.299 0.1444 0.158 1.234 2.21 0.1798 −0.1465 0.411 0.5087 3.457 1.745 3.551 −0.2846 0.158 2.62 3.53 3.728 3.149 0.2238 −0.9861 −0.3033 3.286 −0.07757 2.736 3.579 2.466 1.495 2.523 3.703 3.77 203628_at Human insulin-like growth factor 1 receptor mRNA, 3′ sequence, mRNA sequence 2.795 2.381 5.773 1.45 3.568 3.288 2.631 2.062 2.515 4.693 2 2.984 3.098 4.667 2.513 2.232 2.442 0.5148 2.452 3.675 4.111 2.55 3.705 1.115 1.538 1.731 2.76 3.559 2.259 1.855 0.6405 3.657 4.928 2.664 6.732 6.752 0.5081 2.53 1.503 1.872 4.124 1.466 3.48 2.903 0.2213 3.556 1.22 1.193 3.206 −0.1502 0.07299 0.3962 0.5347 0.7098 0.06693 0.09198 0.3905 −0.02844 −0.009415 1.025 0.7389 2.194 −0.4784 1.723 0.222 0.05793 0.573 3.054 1.338 0.6058 1.426 1.54 0.9868 0.84 0.1264 0.2324 −0.258 1.21 −0.8171 1.998 1.449 −0.1467 0.3772 1.21 −0.4615 1.451 0.1205 −0.1947 −0.9146 1.441 −0.8475 0.04923 0.4557 −2.688 0.2235 0.5537 205307_s_at kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) −0.117 −1.011 −2.489 −0.9037 −1.085 −1.12 −1.219 −1.735 −1.829 −1.721 −1.433 −0.02038 1.167 −1.694 −1.571 1.055 −2.743 0.03987 0.01731 0.1225 0.1203 −1.484 −0.591 −1.35 −0.2275 0.7435 −1.218 −0.4883 −0.8609 −0.7848 −0.2848 −1.499 −0.3403 −1.388 −0.9036 −0.3888 −0.4186 −1.082 −1.261 −1.201 −0.1329 −1.222 −1.679 −0.2855 0.5551 −1.587 −0.1132 −1.485 −1.13 −0.7033 −0.7773 0.7705 0.008025 −0.2992 0.06924 −0.3291 −2.038 −1.017 −3.967 −0.4769 0.8039 −1.589 −0.7423 −0.4919 −1.328 0.2971 −1.549 −0.7277 1.643 −1.604 0.5154 −0.09918 −0.6515 −0.8327 −0.986 −0.04337 −0.95 −0.273 −0.3601 −2.266 1.182 0.7985 −0.8065 1.063 2.302 −0.6945 −1.219 0.9502 −0.894 0.7855 −1.668 0.1515 −0.3956 −1.677 0.22 1.595 210761_s_at growth factor receptor-bound protein 7 0.4452 1.205 1.412 2.858 1.493 1.508 0.3961 0.7703 1.033 0.922 0.4947 1.016 1.668 1.669 2.906 1.568 0.889 3.42 1.335 0.6151 0.7453 0.6185 1.248 1.748 2.238 0.6557 0.7697 1.296 4.588 0.7527 0.5559 0.7794 0.9863 1.981 1.503 0.3864 0.5489 3.704 0.7039 1.561 0.9271 0.6039 0.9461 1.471 3.699 1.334 1.981 0.6054 0.5662 1.051 1.677 1.507 3.042 1.307 4.472 1.189 0.7615 0.228 0.6253 3.214 1.966 0.6688 2.263 3.093 2.839 1.988 1.721 1.684 0.6625 1.159 2.94 1.063 0.1599 1.04 0.2849 3.697 2.31 3.887 0.6321 0.7463 3.728 5.268 3.912 3.666 1.984 0.7088 0.5511 3.982 5.042 4.321 4.339 4.248 2.174 3.317 4.032 4.736 210930_s_at v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) −0.8461 −2.708 −0.9694 0.3187 −1.475 −1.568 0.3559 −1.343 −2.559 −0.9886 −1.727 −1.466 −0.1998 −0.8977 0.3377 −0.3748 −1.943 1.36 −1.455 −1.361 −1.218 −1.374 −0.4494 1.16 0.7238 −0.4209 −2.201 −0.4352 1.833 −1.829 −0.6478 −4.138 −0.5983 0.6215 −1.066 −1.07 −0.332 1.556 −0.5345 −0.8175 −0.2384 −1.649 −0.837 0.487 1.322 −0.7451 0.7285 −0.9136 −1.812 −3.225 −0.1626 −1.19 1.542 −0.4326 1.705 0.2116 −0.2503 −1.408 −1.292 1.544 −0.8231 −1.735 0.4762 0.09548 −0.7243 −0.7869 −1.927 −1.524 −2.637 −4.457 −0.278 −2.773 −2.013 −1.611 −2.056 1.532 0.08922 2.774 −0.2269 −1.08 1.078 2.7 1.397 1.554 −1.5 −0.9627 −0.8952 2.069 1.728 3.212 3.121 3.149 1.108 −0.7891 0.9288 2.864 211657_at carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen) 3.887 1.127 5.069 1.162 4.256 2.372 0.06854 2.496 0.534 1.805 0.6949 4.237 3.755 −0.05911 1.471 1.388 1.548 1.032 4.176 0.407 3.742 3.638 4.006 3.88 5.988 1.433 0.1368 2.179 3.537 0.7946 0.4718 3.327 −0.02141 1.842 0.3149 5.084 0.3826 1.889 −0.9834 2.416 0.3955 0.08346 1.603 2.92 3.158 0.7611 5.397 −0.485 0.3396 0.1982 0.2382 1.376 4.494 0.6605 4.674 4.38 −0.2242 0.2056 −0.3151 3.863 0.983 0.8939 1.474 0.5326 3.265 −0.034 −0.8774 −0.5614 2.687 5.257 4.683 0.7389 0.7168 0.8051 4.189 4.894 4.905 1.134 0.431 0.5341 3.92 5.643 4.536 4.869 3.96 0.6223 5.275 4.33 3.687 4.673 0.2819 1.224 2.126 5.62 3.871 0.6072 213557_at ESTs, Weakly similar to ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome; Ubiquitously transcribed TPR gene on Y chromosome [Homo sapiens] [H. sapiens] 1.252 1.184 0.5043 3.153 1.387 1.868 0.5293 −0.2155 0.3275 0.5276 1.395 1.851 1.543 0.5434 2.397 1.591 0.1861 1.623 1.723 0.7596 0.5377 0.3335 1.596 2.154 1.513 1.603 0.1632 1.181 3.969 0.5737 1.136 2.645 0.6143 2.339 0.2645 0.7221 0.6219 3.499 0.5513 1.099 0.9166 1.378 0.6302 0.9299 3.592 0.9732 3.427 0.7249 0.7654 0.586 1.397 −1.58 3.088 0.7145 4.663 0.5107 1.368 1.251 0.8759 1.862 2.072 1.048 0.8533 3.836 2.693 4.055 1.126 0.493 0.3712 1.462 1.211 0.621 1.516 0.4326 1.09 2.63 2.419 0.667 0.5337 0.3296 3.749 3.494 3.834 3.956 1.295 −0.3071 0.5377 0.8307 1.086 2.534 3.733 3.321 2.127 0.05067 3.98 4.461 214451_at transcription factor AP-2 beta (activating enhancer binding protein 2 beta) −3.097 2.467 −3.372 3.439 0.1365 −1.298 2.39 1.441 2.839 2.516 −1.258 −2.597 −0.5943 1.978 −0.9813 −1.202 1.496 3.43 3.001 −1.562 2.541 −4.519 2.889 0.6659 1.661 −2.472 1.623 3.059 −2.935 3.575 1.469 −4.59 3.603 3.517 −3.813 −0.1878 4.003 −0.4031 0.88 2.51 −4.28 2.753 1.234 −4.588 3.173 −4.705 1.066 −1.809 1.967 −2.498 1.153 0.279 2.117 3.623 −0.005383 1.745 −4.141 −1.479 −1.257 1.798 4.45 −1.547 2.506 3.646 −3.226 −0.913 −3.058 −3.123 3.658 −1.289 3.548 −0.2634 −1.531 −4.923 2.247 1.723 −2.025 3.197 −2.015 −0.7008 4.068 3.333 −1.154 4.028 3.88 0.3311 3.34 2.444 2.631 3.682 3.38 3.92 3.618 4.305 3.96 4.973 215465_at ATP-binding cassette, sub-family A (ABC1), member 12 −5.53 −0.2993 −2.982 −1.196 −1.515 −1.129 1.018 −2.386 −0.3181 −1.932 −1.838 0.7215 −1.211 −1.273 −1.483 −0.995 −1.928 −1.288 −1.39 −0.7415 −0.23 −2.464 −1.478 −0.2715 −1.114 −2.064 1.22 −2.498 −0.9399 −2.507 −0.4786 −2.321 −0.5358 −2.004 −2.388 −2.234 0.078 −1.043 1.185 −1.93 −1.992 −2.169 −2.156 −2.18 0.381 −4.889 1.702 −1.345 −1.946 −1.149 −0.7878 −0.6671 −1.429 −0.559 −1.242 −2.897 −2.329 −1.631 −2.476 −0.6065 0.4199 −2.905 −0.8082 −1.942 −1.804 −1.404 −1.384 −3.471 0.2961 −0.6596 −0.5091 −2.246 −2.386 −2.697 −1.245 0.4357 −0.7417 −0.01172 −1.168 −2.224 −0.5227 1.617 −0.04832 0.4729 −0.4882 −2.002 −0.5482 1.449 −1.664 0.7275 0.8683 −2.091 0.14 0.4634 1.916 0.7919 219429_at fatty acid hydroxylase −1.539 −0.2486 −0.06329 −0.606 −1.426 −1.273 0.05695 0.4841 0.3636 −0.7702 −1.403 −0.7 −1.611 −0.5367 0.6557 −0.5048 −0.9159 0.8194 −1.687 −1.037 −0.6167 −0.1531 −1.306 0.1918 −0.531 0.2454 0.7654 −1.344 0.7986 0.2327 −0.9519 −0.8758 −1.052 −0.6758 0.8207 −0.1432 −0.4994 −0.0002446 −0.2944 −1.152 −0.2746 −1.314 0.3005 −0.5842 0.218 −0.5254 −0.7197 −0.6967 −0.2 −0.8899 −0.2978 0.2625 1.562 −1.044 1.383 −0.5091 −0.3997 −0.8286 −3.217 −0.2482 0.5994 0.06282 0.06886 0.1471 0.9134 0.1739 0.6888 −1.575 0.3812 −0.6085 0.7442 −0.7528 −0.5949 −0.4236 −0.7073 1.218 −0.4363 1.209 0.3444 −0.969 0.2863 0.9532 0.7178 1.296 0.6456 −0.4466 1.152 0.4512 1.933 1.497 −0.3116 0.1834 0.142 1.228 1.876 1.35 220149_at hypothetical protein FLJ22671 −0.585 −1.416 −0.7662 2.221 −0.3646 −0.8895 −0.6838 −0.5557 −0.4347 −0.4597 −0.07175 −0.09613 −0.4148 −0.781 −1.112 −0.482 −1.328 −0.6111 −2.445 −1.028 −0.6113 −0.08989 −1.397 −0.5025 −0.3443 −1.424 −0.3695 −0.8427 0.4616 −1.052 −1.163 −0.9368 −0.3882 0.7431 −0.04467 −0.4188 −0.7193 2.204 −1.393 −0.7435 −1.423 −0.5707 −0.4196 −0.6552 2.686 −0.6905 4.914 −0.3156 −0.9062 −0.1168 0.2261 0.1723 0.386 1.191 2.885 −0.7671 −2.42 −0.2398 −1.799 2.044 0.8819 −0.3224 3.604 1.023 3.736 2.807 −0.5473 −1.357 0.3665 −0.2828 −0.246 −0.01971 0.4476 −0.5921 −0.2366 1.906 −0.3266 2.079 0.2249 −0.5295 0.08667 2.691 1.636 1.349 −0.3243 −1.536 1.435 4.099 −0.8161 1.734 2.641 1.301 1.355 −1.242 1.708 3.096 39248_at aquaporin 3 0.4769 −0.2623 −0.7927 1.948 0.03186 2.194 0.6044 2.335 −0.1663 0.4244 1.476 3.025 0.6734 2.102 3.241 −0.5173 0.8267 3.789 2.556 −0.07496 2.804 1.786 −1.024 0.4586 2.795 0.6762 0.07351 0.3396 0.4198 0.7147 1.677 2.114 −0.1301 0.06363 3.336 3.314 0.1946 1.919 −0.1613 0.8785 −0.1946 −0.1926 −1.876 3.881 0.3148 −1.082 −0.852 0.0508 0.3455 −0.9268 0.2052 0.2611 0.8294 2.1 1.987 3.696 0.8302 1.104 −1.175 3.041 0.07521 3.434 3.543 0.13 1.305 0.1424 2.271 1.841 0.7022 4.044 4.959 0.2898 0.4821 1.642 0.9258 1.169 −0.382 −0.8969 0.8155 1.156 3.712 2.333 1.722 1.466 3.247 1.128 1.167 3.68 4.088 4.324 −0.5153 2.505 5.002 0.05894 5.292 0.9251

TABLE S9 Weighted Voting parameters for mean (μ) and standard deviation (σ) of expression data for Table A4 (common-13) geneset Full Length Ref. High-Confidence Low-confidence Probe_ID Gene Name Sequences Unigene mean SD mean SD Upregulated in Low Confidence Tumours 201525_at apolipoprotein D NM_001647 Hs.75736 3.213993 1.711066 4.43395 2.23157 202991_at START domain containing 3 NM_006804 Hs.77628 0.838735 1.186229 2.215114 1.621765 205307_s_at kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) NM_003679 Hs.107318 −0.75339 0.924201 0.105819 1.199695 210761_s_at growth factor receptor-bound protein 7 NM_005310 Hs.86859 1.512564 1.051211 3.500556 1.421506 210930_s_at v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, NM_004448 Hs.323910 −0.71309 1.339254 1.297613 1.591897 neuro/glioblastoma derived oncogene homolog (avian) 211657_at carcinoembryonic antigen-related cell adhesion molecule 6 NM_002483 Hs.73848 1.948209 1.842322 3.452838 1.859184 (non-specific cross reacting antigen) 213557_at ESTs, Weakly similar to ubiquitously transcribed — Hs.14691 1.359728 1.098941 2.417623 1.605763 tetratricopeptide repeat gene, Y chromosome; Ubiquitously transcribed TPR gene on Y chromosome [Homo sapiens] [H. sapiens] 214451_at transcription factor AP-2 beta (activating enhancer binding NM_003221 Hs.33102 0.234429 2.657284 3.171194 1.547226 protein 2 beta) 215465_at ATP-binding cassette, sub-family A (ABC1), member 12 NM_015657 Hs.134585 −1.35669 1.237705 0.067599 1.228661 219429_at fatty acid hydroxylase — Hs.249163 −0.32527 0.827988 0.809581 0.722212 220149_at hypothetical protein FLJ22671 NM_024861 Hs.193745 −0.05674 1.363225 1.200829 1.596251 39248_at aquaporin 3 NM_004925 Hs.234642 1.076674 1.458035 2.508421 1.755277 Up-regulated in High Confidence tumours 203628_at Human insulin-like growth factor 1 receptor mRNA, 3′ — Hs.405998 1.956068 1.625758 0.129864 1.072433 sequence, mRNA sequence

TABLE A1 SAM (Significance Analysis of Microarrays): At a FDR (False-discovery rate) of <15%, a total of 86 up-regulated and 2 down regulated genes in low-confidence tumors were identified. Using this gene set, the LOOCV assay produced a classification accuracy of 84%. q-value Gene Name Score(d) (%) Unigene Full Length Ref. Sequences Genes up-regulated in Low-confidence tumors 206793_at 4.1852709 1.3837984 Hs.1892 NM_002686 // phenylethanolamine N-methyltransferase 211237_s_at 4.071839 1.3837984 Hs.165950 NM_002011 // fibroblast growth factor receptor 4 isoform 1 precursor /// NM_022963 // fibroblast growth factor receptor 4 isoform 2 precursor 210761_s_at 3.9001438 1.3837984 Hs.86859 NM_005310 // growth factor receptor-bound protein 7 206164_at 3.8109161 1.3837984 Hs.241551 NM_006536 // calcium activated chloride channel 2 204913_s_at 3.4806716 1.3837984 Hs.32964 NM_003108 // SRY (sex determining region Y)-box 11 210930_s_at 3.4544924 1.3837984 Hs.323910 NM_004448 // v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog 204910_s_at 3.3311974 1.3837984 Hs.321576 NM_006458 // tripartite motif-containing 3 isoform alpha /// NM_033278 // tripartite motif- containing 3 isoform beta /// NM_033279 // tripartite motif-containing 3 isoform gamma 214451_at 3.2935388 1.3837984 Hs.33102 NM_003221 // transcription factor AP-2 beta (activating enhancer binding protein 2 beta) 217562_at 3.2344498 1.3837984 Hs.106642 — 217276_x_at 3.0703975 1.3837984 Hs.301947 NM_014509 // kraken-like 215686_x_at 3.0323791 1.3837984 — — 215559_at 3.0225718 1.3837984 Hs.274260 NM_001171 // ATP-binding cassette, sub-family C, member 6 206827_s_at 2.9342047 1.3837984 Hs.302740 NM_014274 // transient receptor potential cation channel, subfamily V, member 6 /// NM_018646 // transient receptor potential cation channel, subfamily V, member 6 208893_s_at 2.9089684 1.3837984 Hs.180383 NM_001946 // dual specificity phosphatase 6 isoform a /// NM_022652 // dual specificity phosphatase 6 isoform b 203619_s_at 2.8107802 1.3837984 Hs.182859 — 203824_at 2.7813798 1.3837984 Hs.84072 NM_004616 // transmembrane 4 superfamily member 3 221811_at 2.747613 1.3837984 Hs.91668 — 216202_s_at 2.7319622 1.3837984 Hs.59403 NM_004863 // serine palmitoyltransferase, long chain base subunit 2 209757_s_at 2.7152502 1.3837984 Hs.25960 NM_005378 // v-myc myelocytomatosis viral related oncogene, neuroblastoma derived 219429_at 2.665359 1.3837984 Hs.249163 — 215465_at 2.628031 1.3837984 Hs.134585 NM_015657 // ATP-binding cassette, sub-family A, member 12 isoform b /// NM_173076 // ATP-binding cassette, sub-family A, member 12 isoform a 214203_s_at 2.6018018 1.3837984 Hs.343874 NM_005974 // /// NM_016335 // proline dehydrogenase (oxidase) 1 202942_at 2.5652724 1.3837984 Hs.74047 NM_001985 // electron-transfer-flavoprotein, beta polypeptide 205478_at 2.545305 1.3837984 Hs.76780 NM_006741 // protein phosphatase 1, regulatory (inhibitor) subunit 1A 203722_at 2.5390254 1.3837984 Hs.77448 NM_003748 // aldehyde dehydrogenase 4A1 precursor /// NM_170726 // aldehyde dehydrogenase 4A1 precursor 202991_at 2.5022628 1.3837984 Hs.77628 NM_006804 // steroidogenic acute regulatory protein related 205104_at 2.4827654 1.3837984 Hs.323833 NM_014723 // syntaphilin 215659_at 2.4619073 1.3837984 Hs.306777 — 220622_at 2.407245 1.3837984 Hs.114005 NM_024727 // hypothetical protein FLJ23259 208083_s_at 2.3715062 1.3837984 Hs.57664 NM_000888 // integrin, beta 6 206043_s_at 2.3543638 1.3837984 Hs.6168 NM_014861 // KIAA0703 gene product 221345_at 2.3351396 1.3837984 Hs.248056 NM_005306 // G protein-coupled receptor 43 39248_at 2.3213986 1.3837984 Hs.234642 NM_004925 // aquaporin 3 205766_at 2.3057935 1.3837984 Hs.343603 NM_003673 // telethonin 211682_x_at 2.2991204 1.3837984 Hs.137585 NM_053039 // UDP glycosyltransferase 2 family, polypeptide B28 210571_s_at 2.2806771 1.3837984 Hs.24697 XR_000114 // 219233_s_at 2.2752973 1.3837984 Hs.19054 NM_018530 // hypothetical protein PRO2521 204818_at 2.2720676 1.3837984 Hs.155109 NM_002153 // hydroxysteroid (17-beta) dehydrogenase 2 211828_s_at 2.2270979 1.3837984 Hs.170204 — 205916_at 2.2142817 1.3837984 Hs.112408 NM_002963 // S100 calcium-binding protein A7 209522_s_at 2.2117774 1.3837984 Hs.12068 NM_000755 // carnitine acetyltransferase precursor, isoform 1 /// NM_004003 // carnitine acetyltransferase isoform 2 /// NM_144782 // carnitine acetyltransferase precursor, isoform 3 209016_s_at 2.2112214 1.3837984 Hs.23881 — 209505_at 2.2006627 1.3837984 Hs.374991 — 200831_s_at 2.1927228 1.3837984 Hs.119597 NM_005063 // stearoyl-CoA desaturase (delta-9-desaturase) 207802_at 2.1832898 1.3837984 Hs.54431 NM_006061 // specific granule protein (28 kDa) 216633_s_at 2.1766477 1.3837984 Hs.193143 — 214614_at 2.1670563 1.3837984 Hs.37035 NM_005515 // homeo box HB9 204607_at 2.1402505 1.3837984 Hs.59889 NM_005518 // 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial) 220149_at 2.1400852 1.3837984 Hs.193745 NM_024861 // hypothetical protein FLJ22671 219756_s_at 2.1391208 1.3837984 Hs.267038 NM_024921 // premature ovarian failure 1B 213674_x_at 2.1351759 1.3837984 Hs.300697 — 211657_at 2.1231572 1.3837984 Hs.73848 NM_002483 // carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen) 204941_s_at 2.1178907 1.3837984 Hs.87539 NM_000695 // aldehyde dehydrogenase 3B2 214133_at 2.0836401 3.5733527 Hs.99918 — 210663_s_at 2.0766057 3.5733527 Hs.169139 NM_003937 // kynureninase (L-kynurenine hydrolase) 220414_at 2.0543228 3.5733527 Hs.180142 NM_017422 // calmodulin-like skin protein 205808_at 2.0365629 3.5733527 Hs.283664 NM_004318 // aspartate beta-hydroxylase isoform a /// NM_020164 // aspartate beta-hydroxylase isoform e /// NM_032466 // aspartate beta-hydroxylase isoform c /// NM_032467 // aspartate beta-hydroxylase isoform d /// NM_032468 // aspartate beta-hydroxylase isoform b 203365_s_at 2.0185514 3.5733527 Hs.80343 NM_002428 // matrix metalloproteinase 15 preproprotein 206509_at 2.0114514 3.5733527 Hs.99949 NM_002652 // prolactin-induced protein 213557_at 1.9942427 3.5733527 Hs.14691 — 214971_s_at 1.9917977 3.5733527 Hs.2554 NM_003032 // sialyltransferase 1 isoform a /// NM_173216 // sialyltransferase 1 isoform a /// NM_173217 // sialyltransferase 1 isoform b 211899_s_at 1.9768615 4.5901604 Hs.8375 NM_004295 // TNF receptor-associated factor 4 isoform 1 /// NM_145751 // TNF receptor- associated factor 4 isoform 2 220615_s_at 1.9216703 4.5901604 Hs.100895 NM_018099 // hypothetical protein FLJ10462 206915_at 1.8471141 7.400989 Hs.355454 NM_002509 // NK2 transcription factor related, locus 2 201388_at 1.8446012 7.400989 Hs.9736 NM_002809 // proteasome 26S non-ATPase subunit 3 205307_s_at 1.8282052 7.400989 Hs.107318 NM_003679 // kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) 209616_s_at 1.8059335 7.400989 Hs.76688 NM_001266 // carboxylesterase 1 (monocyte/macrophage serine esterase 1) 205910_s_at 1.7828285 7.400989 Hs.406160 NM_001807 // carboxyl ester lipase precursor 201525_at 1.7490382 7.400989 Hs.75736 NM_001647 // apolipoprotein D precursor 201729_s_at 1.7197176 9.106286 Hs.151761 — 204304_s_at 1.6603865 9.106286 Hs.112360 NM_006017 // prominin-like 1 220225_at 1.6559087 9.106286 Hs.196927 NM_016358 // iroquois homeobox protein 4 209560_s_at 1.6357376 10.248328 Hs.169228 NM_003836 // delta-like homolog 207131_x_at 1.6311017 10.248328 Hs.401847 NM_005265 // gamma-glutamyltransferase 1 /// NM_013421 // gamma-glutamyltransferase 1 precursor /// NM_013430 // gamma-glutamyltransferase 1 220972_s_at 1.6233436 10.248328 Hs.307010 NM_030975 // keratin associated protein 9.9 209641_s_at 1.6169812 10.248328 Hs.90786 NM_003786 // ATP-binding cassette, sub-family C, member 3 isoform MRP3 /// NM_020037 // ATP-binding cassette, sub-family C, member 3 isoform MRP3A /// NM_020038 // ATP-binding cassette, sub-family C, member 3 isoform MRP3B 211588_s_at 1.6135313 10.248328 Hs.381618 — 201946_s_at 1.5784917 10.248328 Hs.432970 NM_006431 // chaperonin containing TCP1, subunit 2 (beta) 205029_s_at 1.5779091 10.248328 Hs.26770 NM_001446 // fatty acid binding protein 7, brain 201942_s_at 1.5530281 11.432502 Hs.5057 NM_001304 // carboxypeptidase D precursor 213913_s_at 1.5514129 11.432502 Hs.11912 — 207102_at 1.5436816 11.432502 Hs.201667 NM_005989 // aldo-keto reductase family 1, member D1 214624_at 1.5133976 11.432502 Hs.159309 NM_007000 // uroplakin 1A /// NM_032896 // 206714_at 1.5040028 11.432502 Hs.111256 NM_001141 // arachidonate 15-lipoxygenase, second type 205765_at 1.4589879 12.831585 Hs.104117 NM_000777 // cytochrome P450, family 3, subfamily A, polypeptide 5 213043_s_at 1.4469888 12.831585 Hs.23106 NM_014815 // thyroid hormone receptor-associated protein Genes up-regulated in High-confidence tumours 204286_s_at −3.429773 1.3837984 Hs.96 NM_021127 // phorbol-12-myristate-13-acetate-induced protein 1 203628_at −2.907564 1.3837984 Hs.405998 —

TABLE A2 GR (Gene Ranking by SVM): A total of 251 genes were identified with the ability to classify the HC or LC status of a tumor, with a classification accuracy of 86%. The genes are ranked by their discriminative strength, which is calculated by gene-specific misclassification rate. The Gene Rank-SVM package is provided by GeneData ™ (Basel, Switzerland) Probe ID Gene Description Unigene ID 205225_at estrogen receptor 1 Hs.1657 206165_s_at chloride channel, calcium activated, family member 2 Hs.241551 202917_s_at S100 calcium binding protein A8 (calgranuilin A) Hs.100000 210761_s_at growth factor receptor-bound protein 7 Hs.86859 202376_at serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 Hs.234726 211657_at carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen) Hs.73848 206509_at prolactin-induced protein Hs.99949 201650_at keratin 19 Hs.182265 204734_at keratin 15 Hs.80342 203627_at Human insulin-like growth factor 1 receptor mRNA, 3′ sequence, mRNA sequence Hs.405998 39248_at aquaporin 3 Hs.234642 209603_at GATA binding protein 3 Hs.169946 204508_s_at hypothetical protein FLJ20151 Hs.279916 215470_at Homo sapiens cDNA FLJ36630 fis, clone TRACH2018278, mRNA sequence Hs.14658 203749_s_at retinoic acid receptor, alpha Hs.361071 210930_s_at v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene Hs.323910 homolog (avian) 219233_s_at hypothetical protein PRO2521 Hs.19054 204475_at matrix metalloproteinase 1 (interstitial collagenase) Hs.83169 203875_at SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 Hs.152292 211699_x_at hemoglobin, alpha 1 Hs.272572 205239_at amphiregulin (schwannoma-derived growth factor) Hs.270833 205009_at trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in) Hs.350470 221811_at hypothetical gene MGC9753 Hs.91668 218541_s_at chromosome 8 open reading frame 4 Hs.283683 203628_at Human insulin-like growth factor 1 receptor mRNA, 3′ sequence, mRNA sequence Hs.405998 209301_at carbonic anhydrase II Hs.155097 219263_at hypothetical protein FLJ23516 Hs.9238 203917_at coxsackie virus and adenovirus receptor Hs.79187 203980_at fatty acid binding protein 4, adipocyte Hs.391561 207076_s_at argininosuccinate synthetase Hs.160786 203408_s_at special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA's) Hs.74592 203060_s_at 3′-phosphoadenosine 5′-phosphosulfate synthase 2 Hs.274230 63825_at Similar to hypothetical protein PRO2831 [Homo sapiens], mRNA sequence Hs.406646 222303_at ESTs Hs.292477 211959_at Unknown (protein for IMAGE: 4183312) [Homo sapiens], mRNA sequence Hs.380833 217776_at retinol dehydrogenase 11 (all-trans and 9-cis) Hs.179817 204863_s_at interleukin 6 signal transducer (gp130, oncostatin M receptor) Hs.82065 202887_s_at HIF-1 responsive RTP801 Hs.111244 201841_s_at heat shock 27 kDa protein 1 Hs.76067 207847_s_at mucin 1, transmembrane Hs.89603 215294_s_at SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 Hs.152292 218677_at S100 calcium binding protein A14 Hs.288998 201931_at etectron-transfer-flavoprotein, alpha polypeptide (glutaric aciduria II) Hs.169919 202991_at START domain containing 3 Hs.77628 210633_x_at keratin 10 (epidermolytic hyperkeratosis; keratosis palmaris et plantaris) Hs.99936 203571_s_at adipose specific 2 Hs.74120 220625_s_at E74-like factor 5 (ets domain transcription factor) Hs.11713 205567_at carbohydrate (keratan sulfate Gal-6) sulfotransferase 1 Hs.104576 212202_s_at DKFZP564G2022 protein Hs.16492 202888_s_at alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal Hs.1239 aminopeptidase, CD13, p150) 207023_x_at keratin 10 (epidermolytic hyperkeratosis; keratosis palmaris et plantaris) Hs.99936 204913_s_at SRY (sex determining region Y)-box 11 Hs.32964 204404_at solute carrier family 12 (sodium/potassium/chloride transporters), member 2 Hs.110736 211719_x_at fibronectin 1 Hs.287820 216510_x_at immunoglobulin heavy constant mu Hs.153261 218772_x_at hypothetical protein FLJ10493 Hs.279610 201951_at activated leukocyte cell adhesion molecule Hs.10247 209250_at degenerative spermatocyte homolog, lipid desaturase (Drosophila) Hs.185973 214745_at KIAA1069 protein Hs.193143 201946_s_at chaperonin containing TCP1, subunit 2 (beta) Hs.432970 205916_at S100 calcium binding protein A7 (psoriasin 1) Hs.112408 212736_at hypothetical gene BC008967 Hs.6349 213438_at Homo sapiens cDNA FLJ34019 fis, clone FCBBF2002898, mRNA sequence Hs.7309 205518_s_at cytidine monophosphate-N-acetylneuraminic acid hydroxylase Hs.24697 (CMP-N-acetylneuraminate monooxygenase) 221728_x_at Homo sapiens cDNA FLJ30298 fis, clone BRACE2003172, mRNA sequence Hs.351546 205943_at tryptophan 2,3-dioxygenase Hs.183671 207431_s_at degenerative spermatocyte homolog, lipid desaturase (Drosophila) Hs.185973 209267_s_at BCG-induced gene in monocytes, clone 103 Hs.284205 204018_x_at hemoglobin, alpha 1 Hs.272572 212204_at DKFZP564G2022 protein Hs.16492 202310_s_at collagen, type I, alpha 1 Hs.172928 201998_at sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase) Hs.2554 208792_s_at clusterin (complement lysis inhibitor, SP-40, 40, sulfated glycoprotein 2, testosterone-repressed Hs.75106 prostate message 2, apolipoprotein J) 204731_at transforming growth factor, beta receptor III (betaglycan, 300 kDa) Hs.342874 204881_s_at UDP-glucose ceramide glucosyltransferase Hs.432605 205242_at chemokine (C—X—C motif) ligand 13 (B-cell chemoattractant) Hs.100431 200601_at actinin, alpha 4 Hs.182485 202037_s_at secreted frizzled-related protein 1 Hs.7306 219795_at solute carrier family 6 (neurotransmitter transporter), member 14 Hs.162211 217028_at chemokine (C—X—C motif) receptor 4 Hs.89414 205066_s_at ectonucleotide pyrophosphatase/phosphodiesterase 1 Hs.11951 202357_s_at B-factor, properdin Hs.69771 202743_at phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55, gamma) Hs.372548 203874_s_at SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 Hs.152292 210072_at chemokine (C—C motif) ligand 19 Hs.50002 202990_at phosphorylase, glycogen; liver (Hers disease, glycogen storage disease type VI) Hs.771 206115_at early growth response 3 Hs.74088 205498_at growth hormone receptor Hs.125180 212789_at KIAA0056 protein Hs.13421 222155_s_at putative G-protein coupled receptor GPCR41 Hs.6459 218776_s_at hypothetical protein FLJ23375 Hs.285996 200820_at proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 Hs.78466 203337_x_at integrin cytoplasmic domain-associated protein 1 Hs.173274 214218_a_at Human XIST, coding sequence ‘a’ mRNA (locus DXS399E), mRNA sequence Hs.352403 201729_s_at KIAA0100 gene product Hs.151761 204285_s_at phorbol-12-myristate-13-acetate-induced protein 1 Hs.96 214451_at transcription factor AP-2 beta (activating enhancer binding protein 2 beta) Hs.33102 218313_s_at UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7 (GalNac-T7) Hs.246315 217838_s_at RNB6 Hs.241471 209189_at v-fos FBJ murine osteosarcoma viral oncogene homolog Hs.25647 201131_s_at cadherin 1, type 1, E-cadherin (epithelial) Hs.194657 203058_s_at 3′-phosphoadenosine 5′-phosphosulfate synthase 2 Hs.274230 213557_at ESTs, Weakly similar to ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome; Ubiquitously Hs.14691 transcribed TPR gene on Y chromosome [Homo sapiens] [H. sapiens] 215465_at ATP-binding cassette, sub-family A (ABC1), member 12 Hs.134585 213693_s_at mucin 1, transmembrane Hs.89603 202218_s_at fatty acid desaturase 2 Hs.184641 207175_at adipose most abundant gene transcript 1 Hs.80485 205798_at interleukin 7 receptor Hs.362807 200916_at transgelin 2 Hs.406504 216623_x_at trinucleotide repeat containing 9 Hs.110826 211776_s_at erythrocyte membrane protein band 4.1-like 3 Hs.103839 204472_at GTP binding protein overexpressed in skeletal muscle Hs.79022 220149_at hypothetical protein FLJ22671 Hs.193745 219517_at hypothetical protein FLJ22637 Hs.296178 208653_s_at CD164 antigen, sialomucin Hs.43910 202457_s_at protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha) Hs.272458 222108_at — — 200648_s_at glutamate-ammonia ligase (glutamine synthase) Hs.170171 203287_at ladinin 1 Hs.18141 219429_at fatty acid hydroxylase Hs.249163 212934_at Homo sapiens cDNA FLJ30096 fis, clone BNGH41000045, mRNA sequence Hs.155572 205307_s_at kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) Hs.107318 212686_at KIAA1157 protein Hs.21894 204623_at trefoil factor 3 (intestinal) Hs.82961 209459_s_at NPD009 protein Hs.283675 203827_at hypothetical protein FLJ10055 Hs.9398 201952_at activated leukocyte cell adhesion molecule Hs.10247 202047_s_at chromobox homolog 6 Hs.107374 206036_s_at v-rel reticuloendotheliosis viral oncogene homolog (avian) Hs.44313 205048_s_at phosphoserine phosphatase-like Hs.369508 211527_x_at vascular endothelial growth factor Hs.73793 202660_at minor histocompatibility antigen HA-1 Hs.196914 210495_x_at fibronectin 1 Hs.287820 216442_x_at fibronectin 1 Hs.287820 212865_s_at collagen, type XIV, alpha 1 (undulin) Hs.403836 221765_at UDP-glucose ceramide glucosyltransferase Hs.432605 210538_s_at baculoviral IAP repeat-containing 3 Hs.127799 204151_x_at aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid Hs.306098 dehydrogenase) 213836_s_at hypothetical protein FLJ10055 Hs.9398 202724_s_at forkhead box O1A (rhabdomyosarcoma) Hs.170133 202404_s_at collagen, type I, alpha 2 Hs.179573 202871_at TNF receptor-associated factor 4 Hs.8375 204455_at bullous pemphigoid antigen 1, 230/240 kDa Hs.198689 203640_at muscleblind-like protein MBLL39 Hs.283609 823_at chemokine (C—X3—C motif) ligand 1 Hs.80420 214203_s_at proline dehydrogenase (oxidase) 1 Hs.343874 201963_at fatty-acid-Coenzyme A ligase, long-chain 2 Hs.154890 221730_at collagen, type V, alpha 2 Hs.82985 217047_s_at family with sequence similarity 13, member A1 Hs.177664 203814_s_at NAD(P)H dehydrogenase, quinone 2 Hs.73956 202581_at heat shock 70 kDa protein 1B Hs.274402 218640_s_at phafin 2 Hs.29724 201752_s_at adducin 3 (gamma) Hs.324470 221558_s_at lymphoid enhancer-binding factor 1 Hs.44865 211798_x_at immunoglobulin lambda joining 3 Hs.102950 218400_at 2′-5′-oligoadenylate synthetase 3, 100 kDa Hs.56009 203549_s_at lipoprotein lipase Hs.180878 201525_at apolipoprotein D Hs.75736 203207_s_at likely ortholog of chicken chondrocyte protein with a poly-proline region Hs.170198 201397_at phosphoglycerate dehydrogenase Hs.3343 217996_at pleckstrin homology-like domain, family A, member 1 Hs.82101 211479_s_at 5-hydroxytryptamine (serotonin) receptor 2C Hs.46362 213287_s_at keratin 10 (epidermolytic hyperkeratosis; keratosis palmaris et plantaris) Hs.99936 221517_s_at cofactor required for Sp1 transcriptional activation, subunit 6, 77 kDa Hs.22630 212775_at KIAA0657 protein Hs.6654 217791_s_at pyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase) Hs.114366 215250_at Homo sapiens cDNA FLJ12140 fis, clone MAMMA1000340, mRNA sequence Hs.287491 208733_at RAB2, member RAS oncogene family Hs.78305 219629_at hypothetical protein FLJ20635 Hs.265018 205542_at six transmembrane epithelial antigen of the prostate Hs.61635 208682_s_at melanoma antigen, family D, 2 Hs.4943 218729_at latexin protein Hs.109276 205376_at inositol polyphosphate-4-phosphatase, type II, 105 kDa Hs.153687 203953_s_at claudin 3 Hs.25640 206916_x_at tyrosine aminotransferase Hs.161640 212196_at Homo sapiens mRNA; cDNA DKFZp564F053 (from clone DKFZp564F053), mRNA sequence Hs.71968 211000_s_at interleukin 6 signal transducer (gp130, oncostatin M receptor) Hs.82065 212254_s_at bullous pemphigoid antigen 1, 230/240 kDa Hs.198689 204914_s_at SRY (sex determining region Y)-box 11 Hs.32964 221505_at leucine-rich acidic nuclear protein like Hs.71331 208498_s_at amylase, alpha 1A; salivary Hs.274376 201694_s_at early growth response 1 Hs.326035 201936_s_at eukaryotic translation initiation factor 4 gamma, 3 Hs.25732 203090_at stromal cell-derived factor 2 Hs.118684 37117_at Rho GTPase activating protein 8 Hs.102336 202770_s_at cyclin G2 Hs.429880 209522_s_at carnitine acetyltransferase Hs.12068 212451_at KIAA0256 gene product Hs.118978 201839_s_at tumor-associated calcium signal transducer 1 Hs.692 218309_at hypothetical protein PRO1489 Hs.197922 212450_at KIAA0256 gene product Hs.118978 221589_s_at aldehyde dehydrogenase 6 family, member A1 Hs.293970 217281_x_at immunoglobulin heavy constant gamma 3 (G3m marker) Hs.300697 217388_s_at kynureninase (L-kynurenine hydrolase) Hs.169139 203336_s_at integrin cytoplasmic domain-associated protein 1 Hs.173274 217704_x_at — — 201563_at sorbitol dehydrogenase Hs.878 208151_x_at DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17, 72 kDa Hs.349121 217880_at cell division cycle 27 Hs.406631 213229_at Dicer1, Dcr-1 homolog (Drosophila) Hs.87889 219768_at hypothetical protein FLJ22418 Hs.36563 200602_at amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease) Hs.177486 201082_s_at dynactin 1 (p150, glued homolog, Drosophila) Hs.74617 214774_x_at trinucleotide repeat containing 9 Hs.110826 208654_s_at CD164 antigen, sialomucin Hs.43910 202018_s_at lactotransferrin Hs.105938 212915_at likely ortholog of mouse semaF cytoplasmic domain associated protein 3 Hs.177635 202196_s_at dickkopf homolog 3 (Xenopus laevis) Hs.4909 221024_s_at solute carrier family 2 (facilitated glucose transporter), member 10 Hs.305971 211702_s_at ubiquitin specific protease Hs.155787 205110_s_at fibroblast growth factor 13 Hs.6540 219956_at UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6) Hs.151678 202687_s_at tumor necrosis factor (ligand) superfamily, member 10 Hs.83429 205882_x_at adducin 3 (gamma) Hs.324470 203476_at trophoblast glycoprotein Hs.82128 208991_at Homo sapiens cDNA FLJ35646 fis, clone SPLEN2012743, mRNA sequence Hs.381933 204866_at KIAA0215 gene product Hs.82292 208180_s_at H4 histone family, member H Hs.421737 219410_at hypothetical protein FLJ10134 Hs.104800 209290_s_at nuclear factor I/B Hs.33287 202718_at insulin-like growth factor binding protein 2, 36 kDa Hs.433326 205862_at GREB1 protein Hs.193914 203895_at Homo sapiens mRNA; cDNA DKFZp434E235 (from clone DKFZp434E235), mRNA sequence Hs.348724 212171_x_at vascular endothelial growth factor Hs.73793 217762_s_at RAB31, member RAS oncogene family Hs.223025 208891_at dual specificity phosphatase 6 Hs.180383 221543_s_at chromosome 8 open reading frame 2 Hs.125849 218834_s_at hypothetical protein FLJ20539 Hs.118552 201852_x_at collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) Hs.119571 211965_at zinc finger protein 36, C3H type-like 1 Hs.85155 202015_x_at methionyl aminopeptidase 2 Hs.78935 203348_s_at ets variant gene 5 (ets-related molecule) Hs.43697 202783_at nicotinamide nucleotide transhydrogenase Hs.18136 202403_s_at collagen, type I, alpha 2 Hs.179573 214440_at N-acetyltransferase 1 (arylamine N-acetyltransferase) Hs.155956 211748_x_at prostaglandin D2 synthase 21 kDa (brain) Hs.8272 215073_s_at Homo sapiens, clone IMAGE: 5287010, mRNA, mRNA sequence Hs.288869 215806_x_at T cell receptor gamma constant 2 Hs.274509 205158_at ribonuclease, RNase A family, 4 Hs.283749 221841_s_at Homo sapiens cDNA FLJ38575 fis, clone HCHON2007046, mRNA sequence Hs.376206 214858_at Homo sapiens clone 24566 mRNA sequence Hs.133342 212464_s_at fibronectin 1 Hs.287820 206510_at sine oculis homeobox homolog 2 (Drosophila) Hs.101937 216246_at ribosomal protein S20 Hs.173717 200923_at lectin, galactoside-binding, soluble, 3 binding protein Hs.79339 221989_at ribosomal protein L10 Hs.29797 211284_s_at granulin Hs.180577 209173_at anterior gradient 2 homolog (Xenepus laevis) Hs.91011 200924_s_at solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 Hs.79748 212859_x_at — — 213109_at KIAA0551 protein Hs.170204

TABLE A3 WT (Wilcoxon Test): At a P-value of <0.05 and a >=2-fold change cutoff, a total of 38 genes were identified. This 38 gene set delivered a LOOCV accuracy of 80%. The genes are ranked by their significance (P-value). Probe Gene Description Unigene 210761_s_at growth factor receptor-bound protein 7 Hs.86859 201931_at electron-transfer-flavoprotein, alpha polypeptide (glutaric aciduria II) Hs.169919 219429_at fatty acid hydroxylase Hs.249163 204285_s_at phorbol-12-myristate-13-acetate-induced protein 1 Hs.96 209603_at GATA binding protein 3 Hs.169946 206165_s_at chloride channel, calcium activated, family member 2 Hs.241551 216836_s_at v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene Hs.323910 homolog (avian) 203627_at Human insulin-like growth factor 1 receptor mRNA, 3′ sequence, mRNA sequence Hs.405998 205225_at estrogen receptor 1 Hs.1657 215465_at ATP-binding cassette, sub-family A (ABC1), member 12 Hs.134585 203628_at Human insulin-like growth factor 1 receptor mRNA, 3′ sequence, mRNA sequence Hs.405998 202991_at START domain containing 3 Hs.77628 208891_at dual specificity phosphatase 6 Hs.180383 214451_at transcription factor AP-2 beta (activating enhancer binding protein 2 beta) Hs.33102 204508_s_at hypothetical protein FLJ20151 Hs.279916 202376_at serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 Hs.234726 200832_s_at stearoyl-CoA desaturase (delta-9-desaturase) Hs.119597 205307_s_at kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) Hs.107318 203060_s_at 3′-phosphoadenosine 5′-phosphosulfate synthase 2 Hs.274230 201963_at fatty-acid-Coenzyme A ligase, long-chain 2 Hs.154890 209802_s_at GATA binding protein 3 Hs.169946 211138_s_at kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) Hs.107318 39248_at aquaporin 3 Hs.234642 220149_at hypothetical protein FLJ22671 Hs.193745 55616_at hypothetical gene MGC9753 Hs.91668 205306_x_at kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) Hs.107318 205862_at GREB1 protein Hs.193914 217388_s_at kynureninase (L-kynurenine hydrolase) Hs.169139 204942_s_at aldehyde dehydrogenase 3 family, member B2 Hs.87539 202218_s_at fatty acid desaturase 2 Hs.184641 213557_at ESTs, Weakly similar to ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome; Hs.14691 Ubiquitously transcribed TPR gene on Y chromosome [Homo sapiens] [H. sapiens] 211657_at carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen) Hs.73848 214598_at claudin 8 Hs.162209 218532_s_at hypothetical protein FLJ20152 Hs.82273 202917_s_at S100 calcium binding protein A8 (calgranulin A) Hs.100000 208792_s_at clusterin (complement lysis inhibitor, SP-40, 40, sulfated glycoprotein 2, testosterone-repressed prostate Hs.75106 message 2, apolipoprotein J) 215659_at Homo sapiens cDNA: FLJ21521 fis, clone COL05880, mRNA sequence Hs.306777 201525_at apolipoprotein D Hs.75736

TABLE A4 13 ‘common’ genes among the three gene sets (SAM-88, GR-251, WT-38) were then identified. This 13 member gene achieved a classification accuracy of 84% by LOOCV. In essence, these 13 ‘common genes’ are robust significant markers and can archive comparable performance as other ‘complete’ marker sets. Probe_ID Unigene Full Length Ref. Sequences Location 39248_at Hs.234642 NM_004925 // aquaporin 3 Chr: 9p13 201525_at Hs.75736 NM_001647 // apolipoprotein D precursor Chr: 3q26.2-qter 202991_at Hs.77628 NM_006804 // steroidogenic acute regulatory protein related Chr: 17q11-q12 203628_at Hs.405998 — — 205307_s_at Hs.107318 NM_003679 // kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) Chr: 1q42-q44 210761_s_at Hs.86859 NM_005310 // growth factor receptor-bound protein 7 Chr: 17q21.1 211657_at Hs.73848 NM_002483 // carcinoembryonic antigen-related cell adhesion molecule 6 Chr: 19q13.2 (non-specific cross reacting antigen) 213557_at Hs.14691 — — 214451_at Hs.33102 NM_003221 // transcription factor AP-2 beta (activating enhancer binding protein 2 beta) Chr: 6p12 215465_at Hs.134585 NM_015657 // ATP-binding cassette, sub-family A, member 12 isoform Chr: 2q35 b /// NM_173076 // ATP-binding cassette, sub-family A, member 12 isoform a 219429_at Hs.249163 — Chr: 16q23 220149_at Hs.193745 NM_024861 // hypothetical protein FLJ22671 Chr: 2q37.3 210930_s_at Hs.323910 NM_004448 // v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, Chr: 17q11.2-q12 neuro/glioblastoma derived oncogene homolog

TABLE L1 Look-up ID table for SAM-133 Genes SAM-133 Rank Probe_ID Unigene GenBank 1 205225_at Hs.1657 NM_000125.1 2 209603_at Hs.169946 AI796169 3 204508_s_at Hs.279916 BC001012.1 4 209604_s_at Hs.169946 BC003070.1 5 209602_s_at Hs.169946 AI796169 6 206754_s_at Hs.1360 NM_000767.2 7 203963_at Hs.5338 NM_001218.2 8 214164_x_at Hs.5344 BF752277 9 212956_at Hs.90419 AI348094 10 215867_x_at Hs.5344 AL050025.1 11 210735_s_at Hs.5338 BC000278.1 12 214440_at Hs.155956 NM_000662.1 13 202089_s_at Hs.79136 NM_012319.2 14 210085_s_at Hs.279928 AF230929.1 15 205862_at Hs.193914 NM_014668.1 16 202088_at Hs.79136 AI635449 17 211712_s_at BC005830.1 18 206401_s_at Hs.101174 J03778.1 19 215304_at Hs.159264 U79293.1 20 218195_at Hs.15929 NM_024573.1 21 212195_at Hs.71968 AL049265.1 22 203928_x_at Hs.101174 AI870749 23 209460_at Hs.283675 AF237813.1 24 212960_at Hs.90419 BE646554 25 209443_at Hs.76353 J02639.1 26 209173_at Hs.91011 AF088867.1 27 203071_at Hs.82222 NM_004636.1 28 203571_s_at Hs.74120 NM_006829.1 29 205354_at Hs.81131 NM_000156.3 30 213712_at Hs.30504 BF508639 31 41660_at 32 220744_s_at Hs.70202 NM_018262.1 33 204798_at Hs.1334 NM_005375.1 34 215552_s_at Hs.272288 AI073549 35 209339_at Hs.20191 U76248.1 36 210272_at Hs.330780 M29873.1 37 205186_at Hs.33846 NM_003462.2 38 207414_s_at Hs.170414 NM_002570.1 39 205009_at Hs.1406 NM_003225.1 40 203628_at Hs.239176 H05812 41 211323_s_at Hs.198443 L38019.1 42 201825_s_at Hs.238126 AL572542 43 211234_x_at Hs.1657 AF258449.1 44 209459_s_at Hs.283675 AF237813.1 45 212196_at Hs.71968 AW242916 46 203438_at Hs.155223 AI435828 47 217838_s_at Hs.241471 NM_016337.1 48 204041_at Hs.82163 NM_000898.1 49 203929_s_at Hs.101174 AI056359 50 200670_at Hs.149923 NM_005080.1 51 219414_at Hs.12079 NM_022131.1 52 203627_at Hs.239176 AI830698 53 208451_s_at Hs.278625 NM_000592.2 54 213419_at Hs.324125 U62325.1 55 205768_s_at Hs.11729 NM_003645.1 56 204862_s_at Hs.81687 NM_002513.1 57 210480_s_at Hs.22564 U90236.2 58 205696_s_at Hs.105445 NM_005264.1 59 203685_at Hs.79241 NM_000633.1 60 218976_at Hs.260720 NM_021800.1 61 219197_s_at Hs.222399 AI424243 62 202996_at Hs.82520 NM_021173.1 63 205734_s_at Hs.38070 AI990465 64 211235_s_at Hs.1657 AF258450.1 65 211000_s_at Hs.82065 AB015706.1 66 217190_x_at Hs.247976 S67777 67 202752_x_at Hs.22891 NM_012244.1 68 201754_at Hs.74649 NM_004374.1 69 204623_at Hs.82961 NM_003226.1 70 207038_at Hs.114924 NM_004694.1 71 212637_s_at Hs.324275 AU155187 72 208682_s_at Hs.4943 AF126181.1 73 218502_s_at Hs.26102 NM_014112.1 74 202376_at Hs.234726 NM_001085.2 75 215816_s_at Hs.301011 AB020683.1 76 211233_x_at Hs.1657 M12674.1 77 205081_at Hs.17409 NM_001311.1 78 214428_x_at Hs.170250 K02403.1 79 209696_at Hs.574 D26054.1 80 219682_s_at Hs.332150 NM_016569.1 81 212496_s_at Hs.301011 BE256900 82 203108_at Hs.194691 NM_003979.2 83 206107_at Hs.65756 NM_003834.1 84 218806_s_at Hs.267659 AF118887.1 85 209581_at Hs.37189 BC001387.1 86 213412_at Hs.25527 NM_014428.1 87 212638_s_at Hs.324275 BF131791 88 206469_x_at Hs.284236 NM_012067.1 89 210652_s_at Hs.125783 BC004399.1 90 216381_x_at Hs.284236 AL035413 91 216092_s_at Hs.22891 AL365347.1 92 208788_at Hs.250175 AL136939.1 93 204792_s_at Hs.111862 NM_014714.1 94 207847_s_at Hs.89603 NM_002456.1 95 213201_s_at Hs.73980 AJ011712 96 204497_at Hs.20196 AB011092.1 97 222314_x_at Hs.205660 AW970881 98 222212_s_at Hs.285976 AK001105.1 99 219919_s_at Hs.279808 NM_018276.1 100 214053_at Hs.7888 AW772192 101 204934_s_at Hs.823 NM_002151.1 102 216109_at Hs.306803 AK025348.1 103 203749_s_at Hs.250505 AI806984 104 220329_s_at Hs.238270 NM_017909.1 105 204881_s_at Hs.152601 NM_003358.1 106 208305_at Hs.2905 NM_000926.1 107 209623_at Hs.167531 AW439494 108 218450_at Hs.108675 NM_015987.1 109 204343_at Hs.26630 NM_001089.1 110 219051_x_at Hs.124915 NM_024042.1 111 205471_s_at Hs.63931 AW772082 112 203439_s_at Hs.155223 BC000658.1 113 204863_s_at Hs.82065 BE856546 114 203289_s_at Hs.19699 BE791629 115 221765_at Hs.23703 AI378044 116 219001_s_at Hs.317589 NM_024345.1 117 220581_at Hs.287738 NM_025059.1 118 211596_s_at AB050468.1 119 205645_at Hs.80667 NM_004726.1 120 219663_s_at Hs.157527 NM_025268.1 121 205380_at Hs.15456 NM_002614.1 122 201508_at Hs.1516 NM_001552.1 1 215729_s_at Hs.9030 BE542323 2 201983_s_at Hs.77432 AW157070 3 204914_s_at Hs.32964 AW157202 4 204913_s_at Hs.32964 AI360875 5 205646_s_at Hs.89506 NM_000280.1 6 207030_s_at Hs.10526 NM_001321.1 7 204915_s_at Hs.32964 AB028641.1 8 203021_at Hs.251754 NM_003064.1 9 209800_at Hs.115947 AF061812.1 10 203234_at Hs.77573 NM_003364.1 11 201984_s_at Hs.77432 NM_005228.1

TABLE L2 Lookup table for Table 2 genes Table 2 Probe_ID Unigene GenBank 205225_at Hs.1657 NM_000125.1 205186_at Hs.406050 NM_003462.2 201754_at Hs.351875 NM_004374.1 210085_s_at Hs.279928 AF230929.1 214440_at Hs.155956 NM_000662.1 206754_s_at Hs.1360 NM_000767.2 203749_s_at Hs.361071 AI806984 215552_s_at Hs.239176 AI073549 209443_at Hs.76353 J02639.1 216109_at Hs.306803 AK025348.1 203685_at Hs.79241 NM_000633.1 205862_at Hs.193914 NM_014668.1 217838_s_at Hs.241471 NM_016337.1 209603_at Hs.169946 AI796169 212195_at Hs.71968 AL049265.1 212637_s_at Hs.355977 AU155187 205696_s_at Hs.105445 NM_005264.1 210652_s_at Hs.125783 BC004399.1 205734_s_at Hs.38070 AI990465 211000_s_at Hs.82065 AB015706.1 206107_at Hs.65756 NM_003834.1 203628_at Hs.405998 H05812 204934_s_at Hs.823 NM_002151.1 203071_at Hs.82222 NM_004636.1 204881_s_at Hs.432605 NM_003358.1 210272_at Hs.330780 M29873.1 213201_s_at Hs.73980 AJ011712 206401_s_at Hs.101174 J03778.1 209339_at Hs.20191 U76248.1 208305_at Hs.2905 NM_000926.1 212956_at Hs.90419 AI348094 214164_x_at Hs.279916 BF752277 204343_at Hs.26630 NM_001089.1 203963_at Hs.5338 NM_001218.2 207038_at Hs.114924 NM_004694.1 218195_at Hs.15929 NM_024573.1 220329_s_at Hs.238270 NM_017909.1 218502_s_at Hs.26102 NM_014112.1 219414_at Hs.12079 NM_022131.1 202376_at Hs.234726 NM_001085.2 218806_s_at Hs.267659 AF118887.1 202089_s_at Hs.79136 NM_012319.2 213712_at Hs.432587 BF508639 204497_at Hs.20196 AB011092.1 215616_s_at Hs.301011 AB020683.1 218450_at Hs.294133 NM_015987.1 203438_at Hs.155223 AI435828 208451_s_at Hs.433721 NM_000592.2 205768_s_at Hs.11729 NM_003645.1 219682_s_at Hs.267182 NM_016569.1 204508_s_at Hs.279916 BC001012.1 203963_at Hs.5338 NM_001218.2 209603_at Hs.169946 AI796169 208788_at Hs.250175 AL136939.1 212637_s_at Hs.355977 AU155187 200670_at Hs.149923 NM_005080.1 203571_s_at Hs.74120 NM_006829.1 208682_s_at Hs.4943 AF126181.1 209173_at Hs.91011 AF088867.1 201754_at Hs.351875 NM_004374.1 206469_x_at Hs.284236 NM_012067.1 213412_at Hs.25527 NM_014428.1 222212_s_at Hs.285976 AK001105.1 211323_s_at Hs.198443 L38019.1 209696_at Hs.574 D26054.1 212956_at Hs.90419 AI348094 218195_at Hs.15929 NM_024573.1 202089_s_at Hs.79136 NM_012319.2 209623_at Hs.167531 AW439494 210272_at Hs.330780 M29873.1 204623_at Hs.82961 NM_003226.1 215304_at Hs.159264 U79293.1 214440_at Hs.155956 NM_000662.1 205862_at Hs.193914 NM_014668.1 203108_at Hs.194691 NM_003979.2 207038_at Hs.114924 NM_004694.1 205186_at Hs.406050 NM_003462.2 202752_x_at Hs.22891 NM_012244.1 220744_s_at Hs.70202 NM_018262.1 219414_at Hs.12079 NM_022131.1 204798_at Hs.1334 NM_005375.1 205009_at Hs.350470 NM_003225.1 219051_x_at Hs.124915 NM_024042.1 205471_s_at Hs.63931 AW772082 207847_s_at Hs.89603 NM_002456.1 208451_s_at Hs.433721 NM_000592.2 205081_at Hs.423190 NM_001311.1 209459_s_at Hs.283675 AF237813.1 203071_at Hs.82222 NM_004636.1 209581_at Hs.37189 BC001387.1 204343_at Hs.26630 NM_001089.1 206401_s_at Hs.101174 J03778.1 210480_s_at Hs.385834 U90236.2 201825_s_at Hs.238126 AL572542 203749_s_at Hs.361071 AI806984 218806_s_at Hs.267659 AF118887.1 210652_s_at Hs.125783 BC004399.1 205225_at Hs.1657 NM_000125.1 205768_s_at Hs.11729 NM_003645.1 219682_s_at Hs.332150 NM_016569.1

TABLE L3 Look up table for Table S4 Genes Unigene GenBank Hs.106642 BF589529 Hs.25960 AF320053.1 Hs.1892 NM_002686.1 Hs.289104 NM_014274.1 Hs.165950 NM_002011.2 Hs.173035 AF338650.1 Hs.86859 AB008790.1 Hs.272207 NM_017533.1 Hs.103707 AW192795 Hs.274550 AA074145 Hs.100000 AW238654 Hs.54609 NM_014291.1 Hs.85050 NM_002667.1 Hs.239934 AL022316 Hs.194236 NM_000230.1 Hs.103395 NM_024709.1 Hs.107318 NM_003679.1 Hs.1735 NM_002193.1 Hs.155109 NM_002153.1 Hs.26770 NM_001446.1 Hs.278388 NM_000608.1 Hs.251754 NM_003064.1 Hs.378774 NM_001615.2 Hs.51515 AA053967 Hs.149195 NM_016233.1 Hs.78344 AI889739 Hs.112405 NM_002965.2 Hs.417091 AF052117.1 Hs.57664 NM_000888.3 Hs.154078 NM_004139.1 Hs.100014 NM_007325.1 Hs.193606 AA343027 Hs.202949 AK027231.1 Hs.84072 NM_004616.1 Hs.323910 AF177761.2 Hs.76780 NM_006741.1 Hs.225962 NM_014354.1 Hs.165619 NM_017717.2 Hs.127428 AI246769 Hs.2899 NM_002150.1 Hs.105938 NM_002343.1 Hs.193143 AK022610.1 Hs.1915 NM_004476.1 Hs.160786 NM_000050.1 Hs.23881 AI920979 Hs.3110 NM_000686.2 Hs.180142 NM_017422.2 Hs.169919 NM_000126.1 Hs.112408 NM_002963.2 Hs.96 NM_021127.1 Hs.33846 NM_003462.2 Hs.1360 NM_000767.2 Hs.1657 NM_000125.1 Hs.194689 AF120274.1 Hs.50964 NM_001712.1 Hs.23703 BF970427 Hs.193914 NM_014668.1 Hs.250505 AI806984 Hs.279928 AF230929.1 Hs.156637 NM_012116.1 Hs.169946 AI796169 Hs.4243 NM_024522.1 Hs.111801 NM_015908.1 Hs.155485 NM_005339.2 Hs.99603 NM_024701.1 Hs.55481 NM_003447.1 Hs.306803 AK025348.1 Hs.239176 NM_000875.2 Hs.823 NM_002151.1 Hs.203845 NM_022358.1 Hs.432605 NM_003358.1 Hs.330780 M29873.1 Hs.32981 U38276 Hs.101174 NM_016835.1 Hs.17752 NM_015900.1 Hs.406646 Data not found Hs.351875 NM_004374.1 Hs.20196 AB011092.1 Hs.331584 AF326966.1 Hs.272288 AI073549 Hs.12079 NM_022131.1 Hs.82065 NM_002184.1 Hs.372446 NM_007202.1 Hs.155956 NM_000662.1 Hs.278850 NM_024935.1 Hs.247955 NM_001322.1 Hs.76067 NM_001540.2 Hs.61289 AL157424.1 Hs.334514 NM_032794 Hs.4943 NM_177433 Hs.1892 NM_002686 Hs.321576 NM_006458 Hs.91668 BF033007 Hs.274260 NM_001171 Hs.14368 NM_003022 Hs.86859 NM_005310 Hs.59889 NM_005518 Hs.165950 NM_002011 Hs.83190 NM_004104 Hs.89603 NM_002456 Hs.29724 NM_024613.1 Hs.12068 NM_000755 Hs.279916 NM_017689 Hs.169946 NM_002051 Hs.355977 NM_007013 Hs.33102 NM_003221 Hs.90419 XM_093895 Hs.38972 NM_005727 Hs.31034 NM_003847 Hs.132136 NM_004858 Hs.91668 BF033007 Hs.70604 NM_004496 Hs.234642 NM_004925 Hs.323910 NM_004448 Hs.198443 NM_002222 Hs.197922 NM_018584.1 Hs.87539 NM_000695 Hs.381412 Data not found Hs.180383 NM_001946 Hs.5338 NM_001218 Hs.406515 NM_000903 Hs.8910 NM_020379 Hs.6168 NM_014861 Hs.119597 NM_005063 Hs.574 NM_000507 Hs.326525 NM_009589 Hs.149923 NM_005080 Hs.167531 NM_022132 Hs.184376 NM_003825 Hs.301947 NM_014509 Hs.91011 NM_006408 Hs.114556 NM_017699 Hs.432970 NM_006431 Hs.300697 AK090461 Hs.84072 NM_004616 Hs.878 NM_003104 

1. A method for classifying a breast tumour sample as “low confidence” or “high confidence”, the method comprising providing the expression profile of said breast tumour sample, wherein the expression profile comprises the expression level of a multi-gene classifier comprising at least 5 genes from Table S4, and classifying the tumour as a high or low confidence tumour based on the expression profile, said method optionally comprising determining the estrogen receptor (ER) status of the sample.
 2. A method according to claim 1 comprising determining the estrogen receptor (ER) status of the sample.
 3. A method according to claim 1 comprising the steps of: (a) obtaining expression products from a breast tumour sample obtained from a patient; (b) determining the expression levels of a multi-gene classifier comprising at least 5 genes identified in Table S4 by contacting said expression products with binding members, each binding member being capable of specifically binding to an expression product of the multi-gene classifier; and (c) identifying the presence of a low confidence breast tumour in said patient based on the expression levels.
 4. A method according to claim 3 wherein the expression products are cDNA and the binding members are nucleic acid probes capable of specifically hybridising to the cDNA.
 5. A method according to claim 3 wherein the expression products are RNA or mRNA and the binding members are nucleic acid primers capable of specifically hybridising to the RNA or mRNA and amplifying them in a PCR.
 6. A method according to claim 3 wherein the expression products are polypeptides and the binding members are antibody binding domains capable of binding specifically to the polypeptides.
 7. A method according to claim 3 comprising comparing the binding profile of the expression products from the breast tumour sample under test with a database of other previously obtained profiles and/or a previously determined “standard” profile which is characteristic of the presence of low confidence tumour.
 8. A method according to claim 7 wherein the comparison is performed by a computer programmed to report the statistical similarity between the profile under test and the standard profiles so that a classification may be made.
 9. A method according to claim 1 wherein the step of classifying the breast tumour sample comprises the use of Weighted Voting, Support Vector Machines and/or Hierarchical Clustering.
 10. A method according to claim 1 wherein the multi-gene classifier comprises the genes from Table S4 (a), the genes from Table S4 (b), or a subset of either.
 11. A method according to claim 10 wherein the subset of genes is derived from the upper half of Table S4 (a) or Table S4 (b).
 12. A method according to claim 10 wherein the multi-gene classifier comprises a mixture of upregulated and downregulated genes from Table S4 (a) and/or Table S4 (b).
 13. A method for classifying a breast tumour sample as “low confidence” or “high confidence”, the method comprising providing the expression profile of said breast tumour sample, wherein the expression profile comprises the expression level of a multi-gene classifier comprising at least 5 genes from Table 2, and classifying the tumour as a high or low confidence tumour based on the expression profile, said method optionally comprising determining the estrogen receptor (ER) status of the sample.
 14. A method according to claim 13 comprising determining the estrogen receptor (ER) status of the sample.
 15. A method according to claim 13 comprising the steps of: (a) obtaining expression products from a breast tumour sample obtained from a patient; (b) determining the expression levels of a multi-gene classifier comprising at least 5 genes identified in Table 2 by contacting said expression products with binding members, each binding member being capable of specifically binding to an expression product of the multi-gene classifier; and (c) identifying the presence of a low confidence breast tumour in said patient based on the expression levels.
 16. A method according to claim 15 wherein the expression products are cDNA and the binding members are nucleic acid probes capable of specifically hybridising to the cDNA.
 17. A method according to claim 15 wherein the expression products are RNA or mRNA and the binding members are nucleic acid primers capable of specifically hybridising to the RNA or mRNA and amplifying them in a PCR.
 18. A method according to claim 15 wherein the expression products are polypeptides and the binding members are antibody binding domains capable of binding specifically to the polypeptides.
 19. A method according to claim 15 comprising comparing the binding profile of the expression products from the breast tumour sample under test with a database of other previously obtained profiles and/or a previously determined “standard” profile which is characteristic of the presence of low confidence tumour.
 20. A method according to claim 19 wherein the comparison is performed by a computer programmed to report the statistical similarity between the profile under test and the standard profiles so that a classification may be made.
 21. A method according to claim 13 wherein the step of classifying the breast tumour sample comprises the use of Weighted Voting, Support Vector Machines and/or Hierarchical Clustering.
 22. A method according to claim 13 wherein the multi-gene classifier comprises the genes from Table 2 (a), the genes from Table 2 (b), or a subset of either.
 23. A method according to claim 22 wherein the subset of genes is derived from the upper half of Table 2 (a) or Table 2 (b).
 24. A method according to claim 22 wherein the multi-gene classifier comprises a mixture of upregulated and downregulated genes Table 2 (a) and/or Table 2 (b).
 25. A method for classifying a breast tumour sample as “low confidence” or “high confidence”, the method comprising providing the expression profile of said breast tumour sample, wherein the expression profile comprises the expression level of a multi-gene classifier comprising at least 5 genes from at least one table selected from the group consisting of Table A1, Table A2, Table A3, and Table A4, and classifying the tumour as a high or low confidence tumour based on the expression profile.
 26. A method according to claim 25 comprising the steps of: (a) obtaining expression products from a breast tumour sample obtained from a patient; (b) determining the expression levels of a multi-gene classifier comprising at least 5 genes identified in at least one table selected from the group consisting of Table A1, Table A2, Table A3, and Table A4 by contacting said expression products with binding members, each binding member being capable of specifically binding to an expression product of the multi-gene classifier; and (c) identifying the presence of a low confidence breast tumour in said patient based on the expression levels.
 27. A method according to claim 26 wherein the expression products are cDNA and the binding members are nucleic acid probes capable of specifically hybridising to the cDNA.
 28. A method according to claim 26 wherein the expression products are RNA or mRNA and the binding members are nucleic acid primers capable of specifically hybridising to the RNA or mRNA and amplifying them in a PCR.
 29. A method according to claim 26 wherein the expression products are polypeptides and the binding members are antibody binding domains capable of binding specifically to the polypeptides.
 30. A method according to claim 26 comprising comparing the binding profile of the expression products from the breast tumour sample under test with a database of other previously obtained profiles and/or a previously determined “standard” profile which is characteristic of the presence of low confidence tumour.
 31. A method according to claim 30 wherein the comparison is performed by a computer programmed to report the statistical similarity between the profile under test and the standard profiles so that a classification may be made.
 32. A method according to claim 25 wherein the step of classifying the breast tumour sample comprises the use of Weighted Voting, Support Vector Machines and/or Hierarchical Clustering.
 33. A method according to claim 25 wherein the multi-gene classifier comprises the genes from Table A4 or a subset thereof.
 34. A method of producing a nucleic acid expression profile for a breast tumour sample comprising the steps of (a) isolating expression products from said breast tumour sample; (b) identifying the expression levels of a multi-gene classifier comprising at least 5 genes selected from any one of Table S4, Table 2, Table A1, Table A2, Table A3 and Table A4; and (c) producing from the expression levels an expression profile for said breast tumour sample.
 35. A method according to claim 34 comprising the steps of (a) isolating expression products from a breast tumour sample; (b) contacting said expression products with a multi-gene classifier comprising at least 5 binding members capable of specifically and independently binding to expression products of a plurality of genes selected from Table S4 or Table 2, or independently selected from a table selected from the group consisting of at least one of Table A1, Table A2, Table A3, and Table A4, so as to create a first expression profile of a tumour sample from the expression levels of said multi-gene classifier; (c) comparing the expression profile with an expression profile characteristic of a high confidence tumour and/or a low confidence breast tumour.
 36. An expression profile database comprising a plurality of gene expression profiles of high confidence and/or low confidence breast tumour samples wherein each gene expression profile is derived from a multi-gene classifier comprising at least 5 genes selected from Table S4 or Table 2, or independently selected from a table selected from the group consisting of at least one of Table A1, Table A2, Table A3, and Table A4, and wherein the database is retrievably held on a data carrier.
 37. An expression profile database according to claim 36 wherein the expression profiles making up the database are produced by (a) isolating expression products from said breast tumour sample; (b) identifying the expression levels of a multi-gene classifier comprising at least 5 genes selected from any one of Table S4, Table 2, Table A1, Table A2, Table A3 and Table A4; and (c) producing from the expression levels an expression profile for said breast tumour sample or (a) isolating expression products from a breast tumour sample; (b) contacting said expression products with a multi-gene classifier comprising at least 5 binding members capable of specifically and independently binding to expression products of a plurality of genes selected from Table S4 or Table 2, or independently selected from a table selected from the group consisting of Table A1, Table A2, Table A3 and Table A4, so as to create a first expression profile of a tumour sample from the expression levels of said multi-gene classifier; (c) comparing the expression profile with an expression profile characteristic of a high confidence tumour and/or a low confidence breast tumour.
 38. Apparatus for classifying a breast tumour sample as “high confidence” or “low confidence”, comprising a plurality of binding members attached to a solid support, each binding member being capable of specifically binding to an expression product of a multi-gene classifier comprising at least 5 genes from any one or more of Table S4, Table 2, Table A1, Table A2, Table A3 and Table A4.
 39. Apparatus according to claim 38 comprising binding members capable of binding to expression products of a plurality of genes from each of said Tables.
 40. Apparatus according to claim 38, comprising binding members capable of specifically and independently binding to expression products of all genes identified in Table A4.
 41. Apparatus according to claim 38 comprising a microarray wherein the binding members are nucleic acid sequences capable of capable of specifically hybridising to RNA or mRNA expression products, or cDNA derived therefrom.
 42. A kit for classifying a breast tumour sample as “high confidence” or “low confidence”, said kit comprising a plurality of binding members, each binding member being capable of specifically binding to an expression product of one of a multi-gene classifier comprising at least 5 genes identified in any one or more of Table S4, Table 2, Table A1, Table A2, Table A3 and Table A4, and-a detection reagent.
 43. A kit according to claim 42 wherein the binding members are antibody binding domains or nucleic acid sequences fixed to one or more solid supports.
 44. A kit according to claim 43 comprising a microarray.
 45. A kit according to claim 42 wherein the binding members are nucleic acid primers capable of binding to the expression products, such that they can be amplified in a PCR.
 46. A kit according to claim 42 further comprising one or more standard expression profiles retrievably held on a data carrier for comparison with expression profiles of a test sample.
 47. A kit according to claim 46 wherein the one or more standard expression profiles are produced by (a) isolating expression products from said breast tumour sample; (b) identifying the expression levels of a multi-gene classifier comprising at least 5 genes selected from any one of Table S4, Table 2, Table A1, Table A2, Table A3 and Table A4; and (c) producing from the expression levels an expression profile for said breast tumour sample or (a) isolating expression products from a breast tumour sample; (b) contacting said expression products with a multi-gene classifier comprising at least 5 binding members capable of specifically and independently binding to expression products of a plurality of genes selected from Table S4 or Table 2, or independently selected from a table selected from the group consisting of Table A1, Table A2, Table A3 and Table A4, so as to create a first expression profile of a tumour sample from the expression levels of said multi-gene classifier; (c) comparing the expression profile with an expression profile characteristic of a high confidence tumour and/or a low confidence breast tumour. 